Receptor
PDB id Resolution Class Description Source Keywords
3FSY 1.97 Å EC: 2.3.1.117 STRUCTURE OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE (RV1201C;DAPD) IN COMPLEX WITH SUCCINYL-COA FROM MYCOBACTERT UBERCULOSIS MYCOBACTERIUM TUBERCULOSIS BETA HELIX L BETA H DOMAIN ACYLTRANSFERASE TRANSFERASE
Ref.: THE THREE-DIMENSIONAL STRUCTURE OF A MYCOBACTERIAL PROVIDES INSIGHTS INTO DAPD DIVERSITY AND REVEALS U PARTICULARS ABOUT THE ENZYMATIC MECHANISM. J.MOL.BIOL. V. 389 863 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACY B:332;
C:331;
D:331;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
60.052 C2 H4 O2 CC(=O...
MG A:333;
A:334;
A:335;
A:336;
B:333;
D:332;
D:333;
E:332;
E:333;
E:334;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
MPD A:340;
B:340;
D:340;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
NA A:337;
B:334;
D:334;
E:335;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
SCA A:331;
A:332;
B:331;
E:331;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
867.607 C25 H40 N7 O19 P3 S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3FSY 1.97 Å EC: 2.3.1.117 STRUCTURE OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE (RV1201C;DAPD) IN COMPLEX WITH SUCCINYL-COA FROM MYCOBACTERT UBERCULOSIS MYCOBACTERIUM TUBERCULOSIS BETA HELIX L BETA H DOMAIN ACYLTRANSFERASE TRANSFERASE
Ref.: THE THREE-DIMENSIONAL STRUCTURE OF A MYCOBACTERIAL PROVIDES INSIGHTS INTO DAPD DIVERSITY AND REVEALS U PARTICULARS ABOUT THE ENZYMATIC MECHANISM. J.MOL.BIOL. V. 389 863 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3FSY - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5E3Q - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 5E3R - NPI C7 H13 N O4 C(CCC(=O)O....
3 3FSY - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5E3Q - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 5E3R - NPI C7 H13 N O4 C(CCC(=O)O....
3 3FSY - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SCA; Similar ligands found: 137
No: Ligand ECFP6 Tc MDL keys Tc
1 SCA 1 1
2 GRA 0.899225 1
3 1HE 0.889764 0.955556
4 BCO 0.889764 0.977273
5 MLC 0.889764 1
6 1VU 0.874016 0.966292
7 HGG 0.869231 1
8 IVC 0.860465 0.988506
9 3HC 0.860465 0.988506
10 ACO 0.857143 0.966292
11 HXC 0.856061 0.955556
12 CAA 0.853846 0.988506
13 OXK 0.851562 1
14 TGC 0.849624 0.988636
15 3KK 0.84375 0.977273
16 CO8 0.843284 0.955556
17 CAO 0.84127 0.944444
18 COS 0.84127 0.955056
19 5F9 0.837037 0.955556
20 MYA 0.837037 0.955556
21 MFK 0.837037 0.955556
22 ST9 0.837037 0.955556
23 UCC 0.837037 0.955556
24 DCC 0.837037 0.955556
25 SCO 0.834646 0.977012
26 FAQ 0.834586 0.977273
27 CO6 0.830769 0.977273
28 CMC 0.830769 0.977273
29 MCA 0.825758 0.988636
30 2MC 0.824427 0.934783
31 CMX 0.820312 0.977012
32 FYN 0.815385 0.977012
33 3CP 0.813433 0.977273
34 30N 0.8125 0.894737
35 COO 0.81203 0.977273
36 SCD 0.810606 0.977012
37 SOP 0.80916 0.955056
38 COK 0.80916 0.955056
39 BCA 0.807407 0.966292
40 YNC 0.807143 0.966292
41 MC4 0.80597 0.924731
42 COA 0.80315 0.977012
43 0T1 0.80315 0.954545
44 1CZ 0.80292 0.988636
45 DCA 0.801587 0.932584
46 1GZ 0.8 0.966292
47 COF 0.8 0.934066
48 COW 0.8 0.966292
49 2KQ 0.8 0.977528
50 BYC 0.8 0.977273
51 IRC 0.8 0.988506
52 CS8 0.798561 0.945055
53 HDC 0.792857 0.955556
54 2CP 0.792593 0.966292
55 A1S 0.791045 0.955056
56 ETB 0.787402 0.9
57 FCX 0.78626 0.944444
58 AMX 0.784615 0.965517
59 MCD 0.781955 0.955056
60 2NE 0.776978 0.955556
61 CIC 0.776978 0.977273
62 FAM 0.772727 0.933333
63 4CA 0.768116 0.944444
64 HAX 0.766917 0.933333
65 WCA 0.760563 0.955556
66 1CV 0.760563 1
67 4CO 0.758865 0.944444
68 0FQ 0.758865 0.955056
69 CAJ 0.757353 0.955056
70 CA6 0.755556 0.867347
71 4KX 0.755245 0.945055
72 01A 0.753521 0.913979
73 NMX 0.75 0.884211
74 MRR 0.75 0.955556
75 MRS 0.75 0.955556
76 DAK 0.744828 0.945055
77 0ET 0.741259 0.934066
78 8Z2 0.739726 0.945055
79 S0N 0.739437 0.955056
80 CCQ 0.739437 0.934783
81 YE1 0.733813 0.94382
82 UOQ 0.731034 0.934066
83 NHM 0.731034 0.934066
84 NHW 0.731034 0.934066
85 UCA 0.729032 0.955556
86 HFQ 0.726027 0.934066
87 CA8 0.723404 0.886598
88 1HA 0.72 0.955556
89 NHQ 0.718121 0.965909
90 COT 0.710526 0.955056
91 01K 0.703947 0.955056
92 CA3 0.690323 0.955056
93 CA5 0.679245 0.913979
94 CO7 0.673611 0.977273
95 93P 0.664596 0.966292
96 93M 0.654545 0.966292
97 COD 0.651852 0.965517
98 COA PLM 0.638158 0.923077
99 COA MYR 0.638158 0.923077
100 PLM COA 0.638158 0.923077
101 HMG 0.625 0.965909
102 4BN 0.617143 0.914894
103 5TW 0.617143 0.914894
104 OXT 0.614943 0.914894
105 JBT 0.6 0.915789
106 BSJ 0.585227 0.945055
107 191 0.544872 0.867347
108 PAP 0.540323 0.793103
109 SFC 0.505952 0.955556
110 RFC 0.505952 0.955556
111 PPS 0.503876 0.736842
112 ACE SER ASP ALY THR NH2 COA 0.5 0.933333
113 A3P 0.491935 0.781609
114 0WD 0.476821 0.771739
115 PTJ 0.43662 0.873563
116 3AM 0.432 0.770115
117 AGS 0.425373 0.808989
118 SAP 0.425373 0.808989
119 PUA 0.425 0.802198
120 A22 0.42446 0.795455
121 A2D 0.418605 0.784091
122 PAJ 0.41844 0.885057
123 3OD 0.416667 0.827586
124 ATR 0.414815 0.781609
125 NA7 0.412587 0.83908
126 BA3 0.412214 0.784091
127 ATP 0.410448 0.804598
128 ADP 0.409091 0.804598
129 AP5 0.409091 0.784091
130 B4P 0.409091 0.784091
131 48N 0.407895 0.811111
132 5FA 0.407407 0.804598
133 AQP 0.407407 0.804598
134 A2R 0.407143 0.816092
135 NJP 0.405063 0.788889
136 OAD 0.402778 0.827586
137 WAQ 0.4 0.862069
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3FSY; Ligand: SCA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3fsy.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3FSY; Ligand: SCA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3fsy.bio1) has 8 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3FSY; Ligand: SCA; Similar sites found: 17
This union binding pocket(no: 3) in the query (biounit: 3fsy.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4KBA 1QM 0.03209 0.40008 2.71903
2 4XW2 SIM 0.006176 0.41977 3.0303
3 4XH0 ADP 0.0363 0.4024 3.31325
4 3P13 RIP 0.04407 0.40373 3.47222
5 3R4S SLB 0.01682 0.42166 3.61446
6 3NW7 LGV 0.009876 0.4057 4.51807
7 5A0U CHT 0.02894 0.4024 5.42169
8 2IU8 PLM 0.003221 0.4182 6.92771
9 4MZU COA 0.0002454 0.42667 7.05128
10 4EA7 JB2 0.005138 0.41487 7.83133
11 5FUI APY 0.006617 0.43639 9.63855
12 3VBK 0FX 0.001831 0.43772 13.1707
13 3VBK COA 0.002332 0.4303 13.1707
14 1HV9 COA 0.001291 0.42906 14.4578
15 3FS8 ACO 0.01611 0.403 15.7509
16 4AAW R84 0.001082 0.43216 15.9639
17 1KRR ACO 0.001404 0.42324 17.2414
Pocket No.: 4; Query (leader) PDB : 3FSY; Ligand: SCA; Similar sites found: 208
This union binding pocket(no: 4) in the query (biounit: 3fsy.bio3) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KPE TM3 0.0005778 0.49346 None
2 1BTN I3P 0.02039 0.46096 None
3 1UO5 PIH 0.02642 0.44609 None
4 1NU4 MLA 0.002776 0.44344 None
5 1UO4 PIH 0.03055 0.4346 None
6 2E1A MSE 0.00962 0.41999 None
7 1UW1 ADP 0.03112 0.40598 None
8 2NLI LAC 0.0001894 0.42288 1.20482
9 2NLI FMN 0.0001868 0.42133 1.20482
10 4TSK NDP 0.0003039 0.41543 1.20482
11 3CI3 3PO 0.0001342 0.42848 1.54639
12 3CI3 5AD 0.0001342 0.42848 1.54639
13 4Q0A 4OA 0.006508 0.40339 1.65563
14 4IMG NGF 0.00376 0.40866 1.70648
15 4HZD COA 0.0004804 0.43744 1.77305
16 2NZ2 ASP 0.00006872 0.52065 1.80723
17 3ZPG 5GP 0.02132 0.43618 1.80723
18 2YIV YIV 0.02417 0.4269 1.80723
19 2Z9V PXM 0.0126 0.41941 1.80723
20 1I2B UPG 0.00277 0.41647 1.80723
21 1I2B USQ 0.00277 0.41647 1.80723
22 1I2B NAD 0.00277 0.41647 1.80723
23 4P4T GDP 0.003774 0.41213 1.80723
24 2GN2 C5P 0.004811 0.41184 1.80723
25 2F2U M77 0.01363 0.4092 1.80723
26 2AG8 NAP 0.004147 0.40379 1.90114
27 1PEA ACM 0.01277 0.44121 2.10843
28 1H16 DTL 0.04086 0.4209 2.10843
29 2ZJF BSU 0.01967 0.40243 2.10843
30 4E28 0MZ 0.03888 0.40145 2.10843
31 4M37 SAH 0.006212 0.40081 2.10843
32 1NNS ASP 0.01627 0.40593 2.14724
33 2DTJ THR 0.01736 0.40474 2.24719
34 4B16 NAG 0.003061 0.49039 2.25564
35 1XX4 BAM 0.005252 0.43912 2.29885
36 2HFK E4H 0.0009527 0.46962 2.40964
37 1TV5 ORO 0.0005001 0.45137 2.40964
38 1TV5 N8E 0.0005028 0.4444 2.40964
39 3RO7 TDR 0.001649 0.41416 2.40964
40 1JQ5 NAD 0.004765 0.41048 2.40964
41 1TV5 A26 0.003049 0.40518 2.40964
42 4WVH ASP HIS ASP ALA HIS ALA 0.02238 0.40397 2.40964
43 4U9W COA 0.009285 0.40102 2.41546
44 1YOA FMN 0.04735 0.4311 2.51572
45 2B7N NTM 0.02686 0.40898 2.5641
46 3U1T MLI 0.04975 0.40541 2.589
47 3E6J DR2 0.03567 0.42736 2.62009
48 3K3G MMU 0.001395 0.46529 2.71084
49 4B9E FAH 0.01212 0.43609 2.71084
50 4FUA PGH 0.001814 0.40027 2.7907
51 1A5Z OXM 0.001477 0.4893 2.82132
52 1A5Z FBP 0.0002973 0.44829 2.82132
53 1O68 KIV 0.006119 0.43349 2.90909
54 3NOJ PYR 0.0003039 0.49533 2.94118
55 3ZF8 GDP 0.003935 0.43199 2.95082
56 1FNZ A2G 0.0001657 0.44853 2.95359
57 2IMP NAI 0.00001175 0.47051 3.01205
58 1SS4 CIT 0.0401 0.44464 3.01205
59 3TFC PEP 0.003914 0.44218 3.01205
60 2GWD GLU 0.005675 0.42995 3.01205
61 1GJW GLC 0.02506 0.42038 3.01205
62 4J7H TLO 0.004123 0.40388 3.01205
63 1F8F NAD 0.0008741 0.40096 3.01205
64 3EJ0 11X 0.0006943 0.47904 3.06122
65 4K30 NLG 0.01832 0.41209 3.125
66 4IAE 1DX 0.0002715 0.41084 3.1746
67 5DRN 5CT 0.002162 0.4939 3.25581
68 1A8S PPI 0.0002155 0.48205 3.2967
69 2ZWS PLM 0.004984 0.48843 3.31325
70 2NVK NAP 0.01735 0.41316 3.31325
71 1AUA BOG 0.02353 0.40718 3.31325
72 1VCO GLN 0.001135 0.40664 3.31325
73 3GJB AKG 0.02311 0.40335 3.31325
74 3NBK PNS 0.0005066 0.40668 3.38983
75 1S8F GDP 0.01176 0.4041 3.38983
76 3V1V GST 0.009091 0.40136 3.4642
77 4M7F BM3 0.001405 0.46209 3.53982
78 1B74 DGN 0.03405 0.41917 3.54331
79 4IXW IXW 0.01791 0.40821 3.54331
80 4RJK PYR 0.01878 0.45479 3.61446
81 4WBD CIT 0.007267 0.45381 3.61446
82 2EB5 OXL 0.007856 0.43936 3.61446
83 2IZ1 ATR 0.01978 0.42012 3.61446
84 2C5S AMP 0.009776 0.41968 3.61446
85 4OB6 S2T 0.005942 0.41206 3.61446
86 4WBD ADP 0.04265 0.40879 3.61446
87 4C2G ALA ALA ALA ALA 0.01992 0.40619 3.61446
88 1V6A TRE 0.03231 0.40522 3.61446
89 2Q28 ADP 0.005138 0.40378 3.61446
90 4AF5 CIT 0.02235 0.41757 3.68421
91 2O66 FLC 0.01454 0.42138 3.7037
92 2F59 INI 0.006653 0.40304 3.82166
93 1MZV AMP 0.01264 0.41058 3.82979
94 4DN8 BMA 0.0007458 0.48817 3.84615
95 1FX8 BOG 0.001034 0.4371 3.91459
96 3VCA PRO 0.002512 0.45368 3.91566
97 2BO4 FLC 0.006112 0.45082 3.91566
98 2YDW WSH 0.009922 0.41503 3.91566
99 4KCT FDP 0.01228 0.40712 3.91566
100 4KCT PYR 0.02529 0.40164 3.91566
101 3LTW HLZ 0.0454 0.40266 3.92857
102 3NGU ADP 0.005248 0.41811 3.97351
103 3SHR CMP 0.009483 0.41586 4.01338
104 2VAR KDF 0.008651 0.41337 4.15335
105 1Y9Q MED 0.006102 0.44461 4.16667
106 3CQ5 PMP 0.005727 0.42978 4.21687
107 3CEV ARG 0.02369 0.40289 4.21687
108 3O2K DST 0.0313 0.40157 4.21687
109 4Q3F TLA 0.003639 0.45534 4.2735
110 1LYX PGA 0.01051 0.40606 4.43548
111 2Q1A 2KT 0.0004062 0.43518 4.51807
112 1T26 NAI 0.0001599 0.44448 4.65839
113 1T26 GBD 0.0001599 0.44448 4.65839
114 2W24 LYS 0.0009521 0.403 4.66667
115 4NTX AMR 0.002231 0.45602 4.81928
116 3VOZ 04A 0.0009964 0.4377 4.81928
117 2OWZ CIT 0.01119 0.432 4.81928
118 1O9U ADZ 0.04091 0.42087 4.81928
119 1YBH FAD 0.001303 0.41357 4.81928
120 2YP9 SIA CMO 0.005548 0.41133 4.81928
121 1SQ5 PAU 0.01174 0.42078 4.87013
122 4B7E OGA 0.02983 0.40684 4.87106
123 2WA4 069 0.01523 0.40327 4.87106
124 3MAG 3MA 0.02462 0.43987 4.88599
125 1YRX FMN 0.01472 0.40019 4.95868
126 3I3X U22 0.00004948 0.40446 5.01931
127 1C1L GAL BGC 0.02537 0.42011 5.10949
128 1WKL ADP 0.006378 0.40371 5.10949
129 1WKL ATP 0.007657 0.40078 5.10949
130 1JOT GAL A2G 0.01083 0.41341 5.26316
131 4JCA CIT 0.004036 0.48371 5.38922
132 1Z42 HBA 0.01113 0.47234 5.42169
133 2WGC SIA GAL BGC 0.01538 0.45987 5.42169
134 1Z42 FMN 0.01169 0.40799 5.42169
135 4QDC ASD 0.00134 0.4029 5.42169
136 2Y6P CTP 0.004426 0.42984 5.55556
137 2HVK TBA 0.006367 0.44373 5.66038
138 1SC3 MLI 0.005371 0.46055 5.68182
139 4Q3S X7A 0.0001321 0.43965 5.72289
140 1SSQ CYS 0.001343 0.43346 5.72289
141 1NF8 BOG 0.02754 0.41833 5.7971
142 1F7K UMP 0.001023 0.40652 5.88235
143 3KMT SAH 0.0105 0.40606 5.88235
144 2JC9 ADN 0.005686 0.43492 6.0241
145 1ZZ7 S0H 0.01599 0.41475 6.06061
146 3SCH TB6 0.03383 0.40887 6.06061
147 1LDM NAD 0.001334 0.40199 6.07903
148 4IEN COA 0.00007692 0.42537 6.13497
149 1JA9 NDP 0.0005679 0.41546 6.20438
150 1VQ2 DDN 0.00594 0.40837 6.21762
151 4OZJ ADP 0.0008257 0.40485 6.29371
152 1RYI GOA 0.005419 0.48479 6.3253
153 3TKA CTN 0.02507 0.45494 6.3253
154 4CML 52N 0.0008131 0.4096 6.3253
155 1ZJ6 G3D 0.00148 0.44482 6.41711
156 4COQ SAN 0.001439 0.47457 6.47773
157 1B55 4IP 0.01264 0.40285 6.50888
158 2ZO9 MLI 0.00598 0.42211 6.56934
159 1LTH NAD 0.0003292 0.41613 6.58307
160 2CE7 ADP 0.003139 0.42702 6.62651
161 4QDF 30Q 0.0007118 0.41139 6.62651
162 3I8T LBT 0.0003752 0.48771 6.70732
163 3OIG NAD 0.0004047 0.41361 6.76692
164 3W8S GSH 0.03686 0.40253 6.79612
165 4N7C AEF 0.01911 0.42625 6.81818
166 1ML4 PAL 0.00186 0.41782 6.81818
167 1O51 ADP 0.00156 0.40535 7.01754
168 2ZSC BTN 0.01309 0.40224 7.0922
169 1ULE GLA GAL NAG 0.04663 0.41203 7.33333
170 1HK8 DGT 0.008448 0.40257 7.53012
171 4OYA 1VE 0.001442 0.41744 7.83133
172 3B9Z CO2 0.0004868 0.497 8.13253
173 4PB2 5UD 0.005064 0.40742 8.13253
174 3I51 45C 0.01451 0.40412 8.14815
175 2FOI JPA 0.007549 0.42005 8.17844
176 1NXJ TLA 0.00002277 0.50272 8.19672
177 3F81 STT 0.001847 0.48431 8.19672
178 1NXJ GLV 0.0009881 0.46291 8.19672
179 1EDO NAP 0.0000836 0.43949 8.19672
180 3GM5 CIT 0.0459 0.40242 8.80503
181 4LO6 SIA GAL 0.0007614 0.49967 8.94737
182 4F8L GAL 0.04609 0.43179 8.96552
183 2OFE NAG 0.02372 0.41632 9.15493
184 1NYT NAP 0.002 0.4019 9.22509
185 1X1T NAD 0.001323 0.40618 9.61539
186 2Y7P SAL 0.02448 0.4064 9.63303
187 1RZM E4P 0.01992 0.42535 9.63855
188 1RZM PEP 0.01813 0.4123 9.63855
189 3R51 MMA 0.006273 0.46463 9.93976
190 3RF4 FUN 0.008184 0.42782 10.3448
191 3QDT A2G GAL 0.007843 0.4521 10.4895
192 3QDY CBS 0.03936 0.41055 10.4895
193 1QO0 BMD 0.009006 0.43652 10.7143
194 1OYB FMN 0.00096 0.41882 10.8434
195 2Z5Y HRM 0.0006877 0.40723 10.8434
196 3NJQ NJQ 0.00151 0.40277 11.399
197 2VQ5 HBA 0.001537 0.48045 11.9403
198 4IU0 ABH 0.001706 0.41383 12.0482
199 1JN2 SFP 0.01648 0.46491 12.6582
200 1TH8 ADP 0.0221 0.40028 12.931
201 2QIA U20 0.003483 0.42123 12.9518
202 4G4S LDZ 0.00742 0.40471 13.4058
203 1H8G CHT 0.04404 0.43297 13.6842
204 2J5S KTA 0.0004786 0.44519 13.6882
205 1Y7P RIP 0.0041 0.46656 13.9013
206 3FS8 TDR 0.00651 0.42067 15.7509
207 1LNX URI 0.006805 0.43142 18.5185
208 4F4S EFO 0.003171 0.44627 26.3158
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