Receptor
PDB id Resolution Class Description Source Keywords
5V3Y 1.98 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF MTB PKS13 THIOESTERASE DOMAIN IN COMPLE INHIBITOR TAM16 MYCOBACTERIUM TUBERCULOSIS THIOESTERASE DOMAIN TAM16 COMPLEX PKS13 MYCOBACTERIUM POSYNTHASE MYCOLIC ACID CONDENSATION TB STRUCTURAL GENOMICSCONSORTIUM TBSGC ALPHA/BETA HYDROLASE THIOESTERASE-TRANSINHIBITOR COMPLEX TRANSFERASE-TRANSFERASE INHIBITOR COMPLE
Ref.: DEVELOPMENT OF A NOVEL LEAD THAT TARGETS M. TUBERCU POLYKETIDE SYNTHASE 13. CELL V. 170 249 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:1802;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
5V8 A:1801;
B:1801;
Valid;
Valid;
none;
none;
ic50 = 0.19 uM
380.437 C22 H24 N2 O4 CNC(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5V3Y 1.98 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF MTB PKS13 THIOESTERASE DOMAIN IN COMPLE INHIBITOR TAM16 MYCOBACTERIUM TUBERCULOSIS THIOESTERASE DOMAIN TAM16 COMPLEX PKS13 MYCOBACTERIUM POSYNTHASE MYCOLIC ACID CONDENSATION TB STRUCTURAL GENOMICSCONSORTIUM TBSGC ALPHA/BETA HYDROLASE THIOESTERASE-TRANSINHIBITOR COMPLEX TRANSFERASE-TRANSFERASE INHIBITOR COMPLE
Ref.: DEVELOPMENT OF A NOVEL LEAD THAT TARGETS M. TUBERCU POLYKETIDE SYNTHASE 13. CELL V. 170 249 2017
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 5V3X ic50 = 0.26 uM I28 C24 H27 N O4 CCOC(=O)c1....
2 5V40 ic50 = 1.57 uM JS1 C20 H21 N O4 CCOC(=O)c1....
3 5V3Y ic50 = 0.19 uM 5V8 C22 H24 N2 O4 CNC(=O)c1c....
4 5V42 ic50 = 0.24 uM I66 C22 H23 N O4 CCOC(=O)c1....
5 5V41 ic50 = 0.71 uM J24 C22 H23 N O5 CCOC(=O)c1....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5V3X ic50 = 0.26 uM I28 C24 H27 N O4 CCOC(=O)c1....
2 5V40 ic50 = 1.57 uM JS1 C20 H21 N O4 CCOC(=O)c1....
3 5V3Y ic50 = 0.19 uM 5V8 C22 H24 N2 O4 CNC(=O)c1c....
4 5V42 ic50 = 0.24 uM I66 C22 H23 N O4 CCOC(=O)c1....
5 5V41 ic50 = 0.71 uM J24 C22 H23 N O5 CCOC(=O)c1....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5V3X ic50 = 0.26 uM I28 C24 H27 N O4 CCOC(=O)c1....
2 5V40 ic50 = 1.57 uM JS1 C20 H21 N O4 CCOC(=O)c1....
3 5V3Y ic50 = 0.19 uM 5V8 C22 H24 N2 O4 CNC(=O)c1c....
4 5V42 ic50 = 0.24 uM I66 C22 H23 N O4 CCOC(=O)c1....
5 5V41 ic50 = 0.71 uM J24 C22 H23 N O5 CCOC(=O)c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5V8; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 5V8 1 1
2 I66 0.517241 0.770492
3 J24 0.451613 0.774194
4 I28 0.4375 0.761905
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5V3Y; Ligand: 5V8; Similar sites found: 64
This union binding pocket(no: 1) in the query (biounit: 5v3y.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VWA PTY 0.01798 0.40458 None
2 2P1C GG3 0.004462 0.44351 1.74825
3 5V4R MGT 0.004385 0.4436 1.85185
4 3O01 DXC 0.0003529 0.49659 2.0979
5 2Q2Y MKR 0.03745 0.40522 2.0979
6 2Q2Y ADP 0.039 0.40522 2.0979
7 4UCC ZKW 0.002462 0.45677 2.14592
8 1YKI NFZ 0.03364 0.4047 2.30415
9 5CDH TLA 0.004284 0.4094 2.44755
10 4DR9 BB2 0.004506 0.40118 2.60417
11 5CX6 CDP 0.002376 0.44348 2.7972
12 3Q8G PEE 0.03465 0.41831 2.7972
13 1XMY ROL 0.009482 0.40669 2.7972
14 3B6O TMP 0.01278 0.40497 2.83401
15 4ORM ORO 0.003245 0.4803 3.14685
16 4ORM 2V6 0.003245 0.4803 3.14685
17 4ORM FMN 0.003245 0.4803 3.14685
18 4OYA 1VE 0.02499 0.43128 3.14685
19 4X8D AVI 0.006204 0.41326 3.14685
20 5TVI O8N 0.003294 0.44864 3.26087
21 1DEK DGP 0.0001036 0.44544 3.3195
22 1RX0 2MC 0.01438 0.41384 3.4965
23 5FPN KYD 0.01722 0.40362 3.4965
24 4V3I ASP LEU THR ARG PRO 0.01472 0.41068 3.50195
25 3G9E RO7 0.002796 0.45903 3.69004
26 2O1V ADP 0.008764 0.40389 3.84615
27 5UGW GSH 0.005154 0.4161 4
28 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.01702 0.40695 4.34783
29 3CHT 4NB 0.01217 0.41153 4.54545
30 4AML GYU 0.003614 0.40836 4.67836
31 2YNC YNC 0.03238 0.40658 4.8951
32 1SBR VIB 0.01452 0.40223 5
33 5CX8 RP3 0.01349 0.40483 5.24476
34 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 0.009185 0.41892 5.26316
35 1C9K 5GP 0.007507 0.40704 5.55556
36 3W54 RNB 0.001388 0.40987 5.59441
37 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.006893 0.42628 5.85774
38 5OCA 9QZ 0.0002952 0.49481 5.94406
39 4MRP GSH 0.00638 0.43285 5.94406
40 5ERM 210 0.007403 0.42371 5.94406
41 4RW3 TDA 0.02953 0.40505 5.94406
42 3AQT RCO 0.009475 0.41456 6.12245
43 5MWE TCE 0.01138 0.40748 6.17284
44 4CPB GAL CN8 0.005547 0.42455 6.61157
45 3ET1 ET1 0.0006481 0.41071 6.64336
46 4YEF 4CQ 0.01409 0.41477 6.74157
47 1M48 FRG 0.01512 0.40136 6.76692
48 3KDU NKS 0.0009533 0.49746 6.85921
49 3G4G D71 0.009605 0.41272 6.99301
50 3G58 988 0.006829 0.40896 6.99301
51 3RLF MAL 0.01296 0.40015 6.99301
52 3ANP DAO 0.007713 0.42584 7.35294
53 3ANP DCC 0.01078 0.42287 7.35294
54 1M2Z BOG 0.004167 0.43224 8.17121
55 3WCA FPS 0.009138 0.42783 8.74126
56 4P6X HCY 0.008816 0.43238 9.01961
57 1GHE ACO 0.009113 0.4207 9.03955
58 5UNJ RJW 0.002115 0.40814 9.38776
59 4MA7 P2Z 0.00478 0.44215 9.64912
60 3SQP 3J8 0.003353 0.43832 10.1399
61 4ZGM 32M 0.01139 0.41516 10.6557
62 5CHR 4NC 0.003489 0.43673 10.9489
63 3WFD AXO 0.003847 0.42623 12.2378
64 3N7S 3N7 0.0117 0.41644 17.3913
Pocket No.: 2; Query (leader) PDB : 5V3Y; Ligand: 5V8; Similar sites found: 21
This union binding pocket(no: 2) in the query (biounit: 5v3y.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.009831 0.41048 None
2 1YKI FMN 0.03485 0.40067 2.30415
3 4UBS DIF 0.02112 0.40231 2.44755
4 5E70 RCD 0.01837 0.41619 2.7972
5 1ZPD CIT 0.01552 0.41313 3.14685
6 5U83 ZN8 0.01368 0.40351 3.77358
7 4RHP PEF 0.002714 0.43498 3.82979
8 3L1N PLM 0.008425 0.41392 4.12371
9 1XZ3 ICF 0.02277 0.41169 5.17241
10 4DXJ IPE 0.01868 0.41456 5.59441
11 4DXJ 0M9 0.01822 0.41268 5.59441
12 4RW3 PLM 0.0315 0.40381 5.94406
13 2X1L MET 0.01743 0.40317 6.29371
14 1XVB 3BR 0.004689 0.4166 6.64336
15 3WUR O4B 0.007917 0.41969 7.01754
16 4COL DTP 0.00219 0.40729 7.34266
17 1OQC FAD 0.02177 0.40343 9.6
18 3E8T UQ8 0.04832 0.4111 10.9091
19 4MGA 27L 0.02394 0.40184 12.549
20 4TV1 36M 0.0136 0.40363 12.749
21 1YRO UDP 0.01616 0.40152 13.0081
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