Receptor
PDB id Resolution Class Description Source Keywords
1KGQ 2 Å EC: 2.3.1.117 CRYSTAL STRUCTURE OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSF COMPLEX WITH L-2-AMINOPIMELATE AND SUCCINAMIDE-COA MYCOBACTERIUM BOVIS LEFT-HANDED PARALLEL BETA HELIX TRANSFERASE
Ref.: ACYL GROUP SPECIFICITY AT THE ACTIVE SITE OF TETRAHYDRIDIPICOLINATE N-SUCCINYLTRANSFERASE. PROTEIN SCI. V. 11 974 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NPI A:301;
Valid;
none;
submit data
175.182 C7 H13 N O4 C(CCC...
SCO A:302;
Valid;
none;
submit data
850.557 C25 H41 N8 O19 P3 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1KGQ 2 Å EC: 2.3.1.117 CRYSTAL STRUCTURE OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSF COMPLEX WITH L-2-AMINOPIMELATE AND SUCCINAMIDE-COA MYCOBACTERIUM BOVIS LEFT-HANDED PARALLEL BETA HELIX TRANSFERASE
Ref.: ACYL GROUP SPECIFICITY AT THE ACTIVE SITE OF TETRAHYDRIDIPICOLINATE N-SUCCINYLTRANSFERASE. PROTEIN SCI. V. 11 974 2002
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1KGT - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 3TDT - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 1KGQ - SCO C25 H41 N8 O19 P3 CC(C)(CO[P....
4 2TDT - NPI C7 H13 N O4 C(CCC(=O)O....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1KGT - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 3TDT - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 1KGQ - SCO C25 H41 N8 O19 P3 CC(C)(CO[P....
4 2TDT - NPI C7 H13 N O4 C(CCC(=O)O....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1KGT - SCA C25 H40 N7 O19 P3 S CC(C)(CO[P....
2 3TDT - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 1KGQ - SCO C25 H41 N8 O19 P3 CC(C)(CO[P....
4 2TDT - NPI C7 H13 N O4 C(CCC(=O)O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NPI; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 NPI 1 1
2 11C 0.677419 0.961538
3 UN1 0.677419 0.961538
4 DLY 0.575758 0.733333
5 API 0.566667 0.888889
6 DHH 0.558824 0.925926
7 LYS 0.558824 0.709677
8 GGL 0.53125 0.923077
9 DGL 0.53125 0.923077
10 GLU 0.53125 0.923077
11 ORN 0.515152 0.7
12 ABH 0.513514 0.625
13 REZ 0.511628 0.787879
14 CBH 0.5 0.83871
15 6HN 0.5 0.619048
16 NLE 0.5 0.7
17 SHR 0.488889 0.83871
18 26P 0.486486 0.862069
19 PML 0.482759 0.666667
20 0L1 0.464286 0.692308
21 ALY 0.463415 0.666667
22 2NP 0.461538 0.78125
23 2JJ 0.459459 0.657895
24 ONH 0.459459 0.621622
25 5OY 0.459459 0.657895
26 EXY 0.452381 0.685714
27 DNN 0.45 0.6875
28 6CL 0.447368 0.857143
29 GLN 0.441176 0.766667
30 DGN 0.441176 0.766667
31 DAB 0.4375 0.625
32 HSE 0.4375 0.709677
33 KAP 0.435897 0.741935
34 CIR 0.435897 0.621622
35 DSD 0.431818 0.657895
36 NVA 0.424242 0.689655
37 HCS 0.424242 0.666667
38 AZ1 0.419355 0.642857
39 3O3 0.418605 0.787879
40 ONL 0.416667 0.766667
41 IKT 0.409091 0.766667
42 CWL 0.409091 0.766667
43 ASP 0.40625 0.785714
44 DAS 0.40625 0.785714
45 5CT 0.404255 0.666667
46 ACA 0.4 0.666667
47 ZGL 0.4 0.741935
Ligand no: 2; Ligand: SCO; Similar ligands found: 217
No: Ligand ECFP6 Tc MDL keys Tc
1 SCO 1 1
2 CMX 0.882353 1
3 0T1 0.864407 0.976744
4 COA 0.864407 0.976744
5 DCA 0.863248 0.954023
6 SCD 0.854839 1
7 ETB 0.847458 0.920455
8 FCX 0.844262 0.965909
9 30N 0.842975 0.893617
10 COS 0.842975 0.954545
11 CAO 0.842975 0.94382
12 AMX 0.842975 0.988235
13 YZS 0.83871 0.865979
14 KGP 0.83871 0.865979
15 SCA 0.834646 0.977012
16 MLC 0.833333 0.977012
17 CMC 0.832 0.977012
18 FAM 0.829268 0.954545
19 ACO 0.829268 0.94382
20 3CP 0.828125 0.977012
21 OXK 0.824 0.977012
22 CA6 0.824 0.865979
23 MCD 0.824 0.977012
24 HAX 0.822581 0.954545
25 KGJ 0.818898 0.893617
26 S0N 0.816794 0.977012
27 3KK 0.816 0.954545
28 FYN 0.816 0.976744
29 YE1 0.8125 0.965517
30 SOP 0.809524 0.954545
31 COK 0.809524 0.954545
32 2CP 0.806202 0.965909
33 CO6 0.80315 0.954545
34 1VU 0.80315 0.94382
35 NMX 0.80315 0.903226
36 GRA 0.801527 0.977012
37 2KQ 0.8 0.955056
38 HGG 0.8 0.977012
39 MCA 0.79845 0.965909
40 2MC 0.796875 0.913043
41 CAJ 0.796875 0.977012
42 BCA 0.793893 0.94382
43 YXS 0.792308 0.865979
44 YXR 0.792308 0.865979
45 3HC 0.790698 0.965517
46 IVC 0.790698 0.965517
47 A1S 0.790698 0.954545
48 BCO 0.790698 0.954545
49 1HE 0.790698 0.933333
50 BYC 0.78626 0.954545
51 COW 0.78626 0.94382
52 CAA 0.784615 0.965517
53 SO5 0.784615 0.876289
54 LCV 0.784615 0.876289
55 COO 0.784615 0.954545
56 TGC 0.781955 0.965909
57 MC4 0.778626 0.903226
58 1CZ 0.776119 0.965909
59 CIC 0.776119 0.977012
60 CA8 0.772727 0.865979
61 1GZ 0.772727 0.94382
62 KGA 0.772727 0.904255
63 COF 0.772727 0.933333
64 IRC 0.772727 0.965517
65 KFV 0.772727 0.875
66 FAQ 0.766917 0.954545
67 4CA 0.766917 0.94382
68 2NE 0.762963 0.933333
69 HXC 0.761194 0.933333
70 1CV 0.759124 0.977012
71 CO8 0.75 0.933333
72 ST9 0.744526 0.933333
73 DCC 0.744526 0.933333
74 4CO 0.744526 0.94382
75 MFK 0.744526 0.933333
76 UCC 0.744526 0.933333
77 0FQ 0.744526 0.954545
78 5F9 0.744526 0.933333
79 MYA 0.744526 0.933333
80 4KX 0.741007 0.923077
81 0ET 0.73913 0.933333
82 01A 0.73913 0.913043
83 CS8 0.733813 0.923077
84 WCA 0.733813 0.933333
85 J5H 0.730496 0.954545
86 UOQ 0.728571 0.933333
87 NHW 0.728571 0.933333
88 NHM 0.728571 0.933333
89 HDC 0.728571 0.933333
90 MRR 0.723404 0.933333
91 HFQ 0.723404 0.933333
92 MRS 0.723404 0.933333
93 DAK 0.71831 0.923077
94 YNC 0.71831 0.94382
95 8Z2 0.713287 0.923077
96 1HA 0.705479 0.933333
97 NHQ 0.703448 0.965517
98 COD 0.698413 0.965116
99 F8G 0.695946 0.913979
100 01K 0.689189 0.954545
101 COT 0.684564 0.954545
102 CCQ 0.676056 0.913043
103 CA3 0.675497 0.954545
104 7L1 0.671642 0.94382
105 RMW 0.664516 0.933333
106 93P 0.660256 0.965909
107 CA5 0.653846 0.913043
108 UCA 0.649682 0.933333
109 CO7 0.64539 0.954545
110 N9V 0.641379 0.922222
111 93M 0.639752 0.965909
112 COA FLC 0.637037 0.942529
113 OXT 0.6 0.893617
114 5TW 0.593023 0.893617
115 4BN 0.593023 0.893617
116 BUA COA 0.589041 0.921348
117 BSJ 0.588235 0.944444
118 PAP 0.582609 0.811765
119 JBT 0.576271 0.894737
120 6NA COA 0.569536 0.901099
121 HMG 0.565789 0.943182
122 DKA COA 0.558442 0.901099
123 DCR COA 0.558442 0.901099
124 X90 COA 0.558442 0.901099
125 DAO COA 0.558442 0.901099
126 MYR COA 0.558442 0.901099
127 EO3 COA 0.558442 0.901099
128 PLM COA 0.558442 0.901099
129 ASP ASP ASP ILE NH2 CMC 0.532934 0.932584
130 A3P 0.530435 0.8
131 PPS 0.528926 0.734043
132 0WD 0.507042 0.788889
133 SFC 0.487805 0.933333
134 RFC 0.487805 0.933333
135 ACE SER ASP ALY THR NH2 COA 0.472826 0.932584
136 MET VAL ASN ALA CMC 0.469945 0.911111
137 PTJ 0.466165 0.894118
138 3AM 0.465517 0.788235
139 HQG 0.457364 0.835294
140 5AD NJS 0.456647 0.913043
141 A22 0.453846 0.813953
142 PUA 0.450331 0.820225
143 A2D 0.45 0.802326
144 PAJ 0.44697 0.905882
145 AGS 0.444444 0.786517
146 ATR 0.444444 0.8
147 3OD 0.444444 0.847059
148 9BG 0.439189 0.788889
149 ADP 0.439024 0.823529
150 ACE MET LEU GLY PRO NH2 COA 0.438776 0.911111
151 UBG 0.437126 0.844444
152 J4G 0.437037 0.870588
153 2A5 0.436508 0.847059
154 A2R 0.435115 0.835294
155 8LE 0.434109 0.870588
156 48N 0.433566 0.829545
157 BA3 0.430894 0.802326
158 NA7 0.42963 0.858824
159 OAD 0.42963 0.847059
160 NJP 0.42953 0.806818
161 F2R 0.42953 0.886364
162 HEJ 0.428571 0.823529
163 ATP 0.428571 0.823529
164 B4P 0.427419 0.802326
165 AP5 0.427419 0.802326
166 WAQ 0.426471 0.882353
167 5FA 0.425197 0.823529
168 AQP 0.425197 0.823529
169 APR 0.425197 0.823529
170 AR6 0.425197 0.823529
171 AN2 0.424 0.813953
172 JNT 0.422222 0.847059
173 8LQ 0.421053 0.858824
174 QA7 0.421053 0.870588
175 M33 0.420635 0.813953
176 9X8 0.419118 0.806818
177 KG4 0.417323 0.825581
178 SRP 0.416667 0.858824
179 ANP 0.415385 0.804598
180 YLB 0.414966 0.930233
181 ADQ 0.414815 0.825581
182 AMO 0.414815 0.858824
183 YLP 0.413793 0.908046
184 TXA 0.413043 0.837209
185 AT4 0.412698 0.795455
186 5AL 0.412214 0.835294
187 V2G 0.412214 0.872093
188 APU 0.412162 0.786517
189 PAX 0.411392 0.793478
190 7D3 0.41129 0.793103
191 AD9 0.410853 0.804598
192 ODP 0.410596 0.78022
193 25L 0.410072 0.813953
194 7D4 0.409449 0.793103
195 CA0 0.409449 0.825581
196 ATF 0.409091 0.795455
197 A2P 0.408 0.788235
198 8QN 0.407407 0.835294
199 NDP 0.406667 0.788889
200 ACP 0.40625 0.825581
201 8LH 0.406015 0.858824
202 ACQ 0.40458 0.825581
203 A1R 0.404412 0.882353
204 ATP A 0.404255 0.770115
205 ATP A A A 0.404255 0.770115
206 FYA 0.402878 0.813953
207 BIS 0.402878 0.818182
208 NB8 0.402878 0.829545
209 1ZZ 0.402878 0.863636
210 AMP 0.401639 0.8
211 A 0.401639 0.8
212 DLL 0.40146 0.813953
213 AHX 0.40146 0.829545
214 00A 0.40146 0.777778
215 XAH 0.401408 0.863636
216 DND 0.401361 0.816092
217 DQV 0.4 0.813953
Similar Ligands (3D)
Ligand no: 1; Ligand: NPI; Similar ligands found: 205
No: Ligand Similarity coefficient
1 MLY 0.9961
2 ARG 0.9877
3 IAR 0.9833
4 DAR 0.9833
5 ILO 0.9807
6 GGB 0.9745
7 MLZ 0.9698
8 VUR 0.9613
9 M3L 0.9598
10 WT2 0.9500
11 4JK 0.9498
12 NOT 0.9487
13 NMM 0.9470
14 FB6 0.9451
15 HAR 0.9442
16 NNH 0.9427
17 HOC 0.9403
18 ZZU 0.9381
19 AHL 0.9342
20 LPA 0.9338
21 GVA 0.9336
22 OOG 0.9294
23 OCA 0.9284
24 ENV 0.9277
25 LPB 0.9272
26 ENW 0.9270
27 2FM 0.9270
28 S2C 0.9247
29 HRG 0.9239
30 DA3 0.9236
31 011 0.9225
32 RED 0.9221
33 JX7 0.9201
34 5AB 0.9197
35 9J6 0.9168
36 2OR 0.9158
37 3KJ 0.9149
38 8AC 0.9147
39 9YT 0.9144
40 Z70 0.9144
41 DA2 0.9140
42 MF3 0.9138
43 CLT 0.9130
44 4TB 0.9126
45 HC4 0.9114
46 4ZD 0.9110
47 SLZ 0.9106
48 EN1 0.9102
49 E8U 0.9100
50 JM2 0.9088
51 PBN 0.9082
52 RGP 0.9080
53 4DI 0.9075
54 TEG 0.9072
55 LYN 0.9071
56 2MR 0.9065
57 FXY 0.9057
58 S0A 0.9056
59 5PV 0.9055
60 11X 0.9050
61 1PS 0.9050
62 G3M 0.9047
63 XOG 0.9046
64 PUE 0.9031
65 TZP 0.9030
66 LUQ 0.9027
67 KLS 0.9023
68 6FG 0.9017
69 VIO 0.9015
70 CUW 0.9013
71 OJD 0.9008
72 AOY 0.9002
73 1HS 0.8999
74 7XA 0.8996
75 DEZ 0.8993
76 M3P 0.8992
77 2J3 0.8986
78 IJ6 0.8982
79 XRX 0.8976
80 3H2 0.8974
81 SB7 0.8973
82 7UC 0.8967
83 L06 0.8966
84 GRQ 0.8965
85 DDK 0.8961
86 DHC 0.8960
87 Q06 0.8951
88 PMV 0.8944
89 F98 0.8941
90 EGV 0.8937
91 AZM 0.8935
92 KNA 0.8932
93 DKA 0.8932
94 6C8 0.8928
95 DHM 0.8926
96 4TP 0.8926
97 58X 0.8925
98 5TO 0.8922
99 AHN 0.8920
100 DIR 0.8914
101 CXP 0.8911
102 N8C 0.8906
103 SPD 0.8901
104 YIH 0.8897
105 KPC 0.8895
106 PAU 0.8893
107 64Z 0.8890
108 A51 0.8886
109 DLT 0.8884
110 5O5 0.8880
111 OC9 0.8873
112 1N5 0.8868
113 IVL 0.8866
114 8SZ 0.8865
115 3YP 0.8855
116 5KJ 0.8854
117 KPV 0.8852
118 TCA 0.8851
119 PA5 0.8841
120 MHN 0.8839
121 P80 0.8838
122 D53 0.8827
123 I38 0.8825
124 DXP 0.8817
125 QH3 0.8816
126 9GB 0.8814
127 GJK 0.8813
128 GLR 0.8813
129 7C3 0.8811
130 DIA 0.8810
131 DXG 0.8805
132 NWH 0.8803
133 4FE 0.8803
134 HE8 0.8799
135 6C4 0.8797
136 AG2 0.8796
137 ODI 0.8796
138 GLY GLY GLY 0.8793
139 XRS 0.8790
140 QFJ 0.8781
141 MVH 0.8780
142 KDG 0.8779
143 3CX 0.8776
144 37E 0.8776
145 O45 0.8776
146 19N 0.8775
147 E4P 0.8774
148 FER 0.8768
149 FOM 0.8764
150 HPL 0.8764
151 HL4 0.8763
152 D10 0.8760
153 YIP 0.8760
154 DER 0.8749
155 3OL 0.8748
156 R10 0.8745
157 CCU 0.8743
158 SHV 0.8742
159 5LD 0.8739
160 RES 0.8738
161 KPA 0.8736
162 JPQ 0.8733
163 J9Y 0.8732
164 OYA 0.8731
165 E79 0.8730
166 KQY 0.8729
167 A5P 0.8724
168 FB5 0.8724
169 NMH 0.8721
170 M1T 0.8720
171 N6C 0.8716
172 HPO 0.8708
173 HGA 0.8695
174 7OD 0.8695
175 RP3 0.8692
176 HPN 0.8688
177 N9J 0.8687
178 SSB 0.8684
179 SNR 0.8683
180 DX5 0.8670
181 CIY 0.8668
182 5XA 0.8663
183 AE3 0.8657
184 5SP 0.8651
185 6Q3 0.8649
186 5DL 0.8636
187 HSA 0.8635
188 4KJ 0.8628
189 PAN 0.8626
190 DMA 0.8621
191 DZA 0.8616
192 6J5 0.8615
193 5RP 0.8603
194 TX4 0.8601
195 BCH 0.8597
196 S7D 0.8592
197 MGB 0.8591
198 Q9Z 0.8583
199 1X4 0.8568
200 N7I 0.8558
201 4U7 0.8554
202 PTU 0.8554
203 C9M 0.8549
204 0A1 0.8532
205 S8V 0.8520
Ligand no: 2; Ligand: SCO; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1KGQ; Ligand: NPI; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1kgq.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1KGQ; Ligand: NPI; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1kgq.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1KGQ; Ligand: NPI; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1kgq.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1KGQ; Ligand: SCO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1kgq.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1KGQ; Ligand: SCO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1kgq.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1KGQ; Ligand: SCO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1kgq.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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