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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
Ligand no: 1; Ligand: NPI; Similar ligands found: 45
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 GLU 0.53125 0.923077
9 DGL 0.53125 0.923077
10 GGL 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 5OY 0.459459 0.657895
25 ONH 0.459459 0.621622
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 HSE 0.4375 0.709677
32 DAB 0.4375 0.625
33 CIR 0.435897 0.621622
34 KAP 0.435897 0.741935
35 DSD 0.431818 0.657895
36 HCS 0.424242 0.666667
37 NVA 0.424242 0.689655
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 DAS 0.40625 0.785714
43 ASP 0.40625 0.785714
44 5CT 0.404255 0.666667
45 ACA 0.4 0.666667
Ligand no: 2; Ligand: SCO; Similar ligands found: 186
No: Ligand ECFP6 Tc MDL keys Tc
1 SCO 1 1
2 CMX 0.882353 1
3 COA 0.864407 0.976744
4 0T1 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 AMX 0.842975 0.988235
10 30N 0.842975 0.893617
11 COS 0.842975 0.954545
12 CAO 0.842975 0.94382
13 SCA 0.834646 0.977012
14 MLC 0.833333 0.977012
15 CMC 0.832 0.977012
16 ACO 0.829268 0.94382
17 FAM 0.829268 0.954545
18 3CP 0.828125 0.977012
19 CA6 0.824 0.865979
20 OXK 0.824 0.977012
21 MCD 0.824 0.977012
22 HAX 0.822581 0.954545
23 S0N 0.816794 0.977012
24 3KK 0.816 0.954545
25 FYN 0.816 0.976744
26 YE1 0.8125 0.965517
27 SOP 0.809524 0.954545
28 COK 0.809524 0.954545
29 2CP 0.806202 0.965909
30 NMX 0.80315 0.903226
31 1VU 0.80315 0.94382
32 CO6 0.80315 0.954545
33 GRA 0.801527 0.977012
34 2KQ 0.8 0.955056
35 HGG 0.8 0.977012
36 MCA 0.79845 0.965909
37 2MC 0.796875 0.913043
38 CAJ 0.796875 0.977012
39 BCA 0.793893 0.94382
40 1HE 0.790698 0.933333
41 A1S 0.790698 0.954545
42 BCO 0.790698 0.954545
43 IVC 0.790698 0.965517
44 3HC 0.790698 0.965517
45 COW 0.78626 0.94382
46 BYC 0.78626 0.954545
47 COO 0.784615 0.954545
48 CAA 0.784615 0.965517
49 TGC 0.781955 0.965909
50 MC4 0.778626 0.903226
51 CIC 0.776119 0.977012
52 1CZ 0.776119 0.965909
53 CA8 0.772727 0.865979
54 1GZ 0.772727 0.94382
55 IRC 0.772727 0.965517
56 COF 0.772727 0.933333
57 4CA 0.766917 0.94382
58 FAQ 0.766917 0.954545
59 2NE 0.762963 0.933333
60 HXC 0.761194 0.933333
61 1CV 0.759124 0.977012
62 CO8 0.75 0.933333
63 DCC 0.744526 0.933333
64 5F9 0.744526 0.933333
65 UCC 0.744526 0.933333
66 MYA 0.744526 0.933333
67 0FQ 0.744526 0.954545
68 ST9 0.744526 0.933333
69 4CO 0.744526 0.94382
70 MFK 0.744526 0.933333
71 4KX 0.741007 0.923077
72 0ET 0.73913 0.933333
73 01A 0.73913 0.913043
74 CS8 0.733813 0.923077
75 WCA 0.733813 0.933333
76 NHW 0.728571 0.933333
77 HDC 0.728571 0.933333
78 UOQ 0.728571 0.933333
79 NHM 0.728571 0.933333
80 MRS 0.723404 0.933333
81 HFQ 0.723404 0.933333
82 MRR 0.723404 0.933333
83 DAK 0.71831 0.923077
84 YNC 0.71831 0.94382
85 8Z2 0.713287 0.923077
86 1HA 0.705479 0.933333
87 NHQ 0.703448 0.965517
88 COD 0.698413 0.965116
89 F8G 0.695946 0.913979
90 01K 0.689189 0.954545
91 COT 0.684564 0.954545
92 CCQ 0.676056 0.913043
93 CA3 0.675497 0.954545
94 7L1 0.671642 0.94382
95 93P 0.660256 0.965909
96 CA5 0.653846 0.913043
97 UCA 0.649682 0.933333
98 CO7 0.64539 0.954545
99 93M 0.639752 0.965909
100 OXT 0.6 0.893617
101 5TW 0.593023 0.893617
102 4BN 0.593023 0.893617
103 BSJ 0.588235 0.944444
104 PAP 0.582609 0.811765
105 JBT 0.576271 0.894737
106 HMG 0.565789 0.943182
107 COA PLM 0.558442 0.901099
108 PLM COA 0.558442 0.901099
109 ASP ASP ASP ILE CMC NH2 0.532934 0.932584
110 A3P 0.530435 0.8
111 PPS 0.528926 0.734043
112 0WD 0.507042 0.788889
113 SFC 0.487805 0.933333
114 RFC 0.487805 0.933333
115 191 0.487179 0.846939
116 ACE SER ASP ALY THR NH2 COA 0.472826 0.932584
117 PTJ 0.466165 0.894118
118 3AM 0.465517 0.788235
119 A22 0.453846 0.813953
120 PUA 0.450331 0.820225
121 A2D 0.45 0.802326
122 PAJ 0.44697 0.905882
123 AGS 0.444444 0.786517
124 SAP 0.444444 0.786517
125 ATR 0.444444 0.8
126 3OD 0.444444 0.847059
127 ADP 0.439024 0.823529
128 2A5 0.436508 0.847059
129 A2R 0.435115 0.835294
130 48N 0.433566 0.829545
131 BA3 0.430894 0.802326
132 NA7 0.42963 0.858824
133 OAD 0.42963 0.847059
134 NJP 0.42953 0.806818
135 F2R 0.42953 0.886364
136 ATP 0.428571 0.823529
137 HEJ 0.428571 0.823529
138 B4P 0.427419 0.802326
139 AP5 0.427419 0.802326
140 WAQ 0.426471 0.882353
141 5FA 0.425197 0.823529
142 AQP 0.425197 0.823529
143 APR 0.425197 0.823529
144 AR6 0.425197 0.823529
145 AN2 0.424 0.813953
146 M33 0.420635 0.813953
147 9X8 0.419118 0.806818
148 SRP 0.416667 0.858824
149 ANP 0.415385 0.804598
150 YLB 0.414966 0.930233
151 ADQ 0.414815 0.825581
152 AMO 0.414815 0.858824
153 YLP 0.413793 0.908046
154 TXA 0.413043 0.837209
155 AT4 0.412698 0.795455
156 5AL 0.412214 0.835294
157 APU 0.412162 0.786517
158 PAX 0.411392 0.793478
159 7D3 0.41129 0.793103
160 AD9 0.410853 0.804598
161 ODP 0.410596 0.78022
162 25L 0.410072 0.813953
163 CA0 0.409449 0.825581
164 7D4 0.409449 0.793103
165 ATF 0.409091 0.795455
166 A A A 0.408759 0.813953
167 A2P 0.408 0.788235
168 8QN 0.407407 0.835294
169 NDP 0.406667 0.788889
170 ACP 0.40625 0.825581
171 ACQ 0.40458 0.825581
172 A1R 0.404412 0.882353
173 ATP A A A 0.404255 0.770115
174 BIS 0.402878 0.818182
175 1ZZ 0.402878 0.863636
176 FYA 0.402878 0.813953
177 NB8 0.402878 0.829545
178 A 0.401639 0.8
179 AMP 0.401639 0.8
180 DLL 0.40146 0.813953
181 00A 0.40146 0.777778
182 AHX 0.40146 0.829545
183 XAH 0.401408 0.863636
184 NXX 0.401361 0.816092
185 DND 0.401361 0.816092
186 DQV 0.4 0.813953
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: 57
This union binding pocket(no: 1) in the query (biounit: 1kgq.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
1 5SXS AMP 1.82482
2 3SHR CMP 1.82482
3 3IWK NAD 2.18978
4 5LX9 OLB 2.55474
5 5WS9 OXL 2.55474
6 4JJF N2I 2.55474
7 2D24 XYS XYS 3.28467
8 5C8W PCG 3.4965
9 2V9M CIT 3.64964
10 1LSH PLD 3.64964
11 4D52 GXL 4.0146
12 4OFG PCG 4.16667
13 5FUI APY 4.54545
14 2O66 FLC 5.18518
15 2EB5 OXL 5.61798
16 5DYO FLU 5.66038
17 4MOB ADP 5.83942
18 1KZL CRM 6.25
19 5UC4 83S 6.36364
20 4KU7 PCG 6.53595
21 6GE9 ACO 6.56934
22 1NE6 SP1 6.93431
23 5HZ9 5M8 7.40741
24 1LNX URI 7.40741
25 5UF1 FUC GAL NAG 8.09717
26 1J2Z SOG 8.14815
27 1MXG ACR 8.75912
28 6GNO XDI 8.88889
29 3MQG UDP UDP 9.89583
30 3MQG UDP 9.89583
31 3MQG U5P 9.89583
32 3MQG ACO 9.89583
33 3FS8 ACO 10.2564
34 3FS8 TDR 10.2564
35 1SSQ CYS 10.9489
36 2WLG SOP 11.1628
37 4M1U A2G MBG 12.8571
38 3PNA CMP 13.6364
39 2HYQ MAN MAN 17.2131
40 2GUD BMA 17.2131
41 2GUC MAN 17.2131
42 2NU5 NAG 17.2131
43 2HYR BGC GLC 17.2131
44 2GUD MAN 17.2131
45 2NUO BGC 17.2131
46 1KRR ACO 17.8832
47 4MZU COA 17.8832
48 1HV9 COA 18.6131
49 3TWD GOB 18.6131
50 4AAW R84 18.9781
51 3VBK COA 19.0244
52 4EA7 COA 19.3431
53 4EA7 JB2 19.3431
54 3I3X U22 21.1679
55 5T2Y 753 23.2323
56 2QIA U20 23.2824
57 4HZD COA 24.0876
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: 55
This union binding pocket(no: 4) in the query (biounit: 1kgq.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 5SXS AMP 1.82482
2 3SHR CMP 1.82482
3 3IWK NAD 2.18978
4 5LX9 OLB 2.55474
5 4JJF N2I 2.55474
6 2D24 XYS XYS 3.28467
7 5C8W PCG 3.4965
8 2V9M CIT 3.64964
9 1LSH PLD 3.64964
10 4D52 GXL 4.0146
11 4OFG PCG 4.16667
12 5FUI APY 4.54545
13 2EB5 OXL 5.61798
14 5DYO FLU 5.66038
15 4MOB ADP 5.83942
16 1KZL CRM 6.25
17 5UC4 83S 6.36364
18 4KU7 PCG 6.53595
19 6GE9 ACO 6.56934
20 1NE6 SP1 6.93431
21 5HZ9 5M8 7.40741
22 1LNX URI 7.40741
23 5UF1 FUC GAL NAG 8.09717
24 1J2Z SOG 8.14815
25 1MXG ACR 8.75912
26 6GNO XDI 8.88889
27 3MQG UDP UDP 9.89583
28 3MQG UDP 9.89583
29 3MQG U5P 9.89583
30 3MQG ACO 9.89583
31 3FS8 ACO 10.2564
32 3FS8 TDR 10.2564
33 1SSQ CYS 10.9489
34 2WLG SOP 11.1628
35 3PNA CMP 13.6364
36 2HYQ MAN MAN 17.2131
37 2GUD BMA 17.2131
38 2GUC MAN 17.2131
39 2NU5 NAG 17.2131
40 2HYR BGC GLC 17.2131
41 2GUD MAN 17.2131
42 2NUO BGC 17.2131
43 1KRR ACO 17.8832
44 4MZU COA 17.8832
45 1HV9 COA 18.6131
46 3TWD GOB 18.6131
47 4AAW R84 18.9781
48 3VBK COA 19.0244
49 3VBK 0FX 19.0244
50 4EA7 JB2 19.3431
51 4EA7 COA 19.3431
52 3I3X U22 21.1679
53 5T2Y 753 23.2323
54 2QIA U20 23.2824
55 4HZD COA 24.0876
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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