Receptor
PDB id Resolution Class Description Source Keywords
2VG0 1.7 Å EC: 2.5.1.68 RV1086 CITRONELLYL PYROPHOSPHATE COMPLEX MYCOBACTERIUM TUBERCULOSIS PEPTIDOGLYCAN SYNTHESIS CELL WALL BIOGENESIS/DEGRADATION SCELL SHAPE TRANSFERASE PRENYLTRANSFERASE
Ref.: THE STRUCTURAL BASIS OF CHAIN LENGTH CONTROL IN RV1 J. MOL. BIOL. V. 381 129 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1258;
B:1258;
B:1259;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
GPP A:1257;
B:1257;
 Valid;
Valid;
 none;
none;
 submit data
314.209 C10 H20 O7 P2 CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VG1 1.7 Å EC: 2.5.1.68 RV1086 E,E-FARNESYL DIPHOSPHATE COMPLEX MYCOBACTERIUM TUBERCULOSIS PEPTIDOGLYCAN SYNTHESIS CELL WALL BIOGENESIS/DEGRADATION SCELL SHAPE TRANSFERASE PRENYLTRANSFERASE
Ref.: THE STRUCTURAL BASIS OF CHAIN LENGTH CONTROL IN RV1 J. MOL. BIOL. V. 381 129 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
2 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
50% Homology Family (28)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 15.4 uM 53Q C26 H28 Cl N O CCN(CC)CCO....
5 5ZHE - HJX C21 H34 O4 CCCCCCCCCC....
6 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
7 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
8 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
9 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
10 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
11 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
12 3WYJ ic50 = 0.36 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
13 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
14 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
15 2VG2 - IPE C5 H12 O7 P2 CC(=C)CCO[....
16 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
17 6IME - GST C10 H20 O6 P2 S CC(=CCCC(=....
18 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
19 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
20 5HC7 - DST C5 H12 O6 P2 S CC(=CCS[P@....
21 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
22 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
23 4U82 ic50 = 1.9 uM FPS C15 H28 O6 P2 S CC(=CCC/C(....
24 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
25 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
26 6SZG - M2K C8 H10 N2 O2 C1CCc2c(c(....
27 6ACS - CIT C6 H8 O7 C(C(=O)O)C....
28 6SZH - M2H C7 H8 N2 Cc1cc([nH]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GPP; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 GPP 1 1
2 ZTP 0.911111 0.95
3 GRG 0.911111 0.974359
4 VTP 0.911111 0.95
5 OTP 0.911111 0.95
6 FPP 0.911111 0.974359
7 HZZ 0.704545 0.921053
8 FFF 0.672727 0.904762
9 FJP 0.659574 0.897436
10 0K3 0.659574 0.875
11 DSL 0.659574 0.875
12 FDF 0.654545 0.880952
13 10E 0.617021 0.717391
14 10D 0.617021 0.804878
15 DMA 0.613636 0.868421
16 H6P 0.595745 0.804878
17 10G 0.583333 0.785714
18 A4S 0.545455 0.711538
19 FPF 0.533333 0.904762
20 2CF 0.533333 0.904762
21 FGG 0.52459 0.904762
22 GST 0.518519 0.878049
23 3E9 0.516129 0.926829
24 ELU 0.507937 0.926829
25 ELR 0.507937 0.926829
26 MGM 0.5 0.745098
27 FPS 0.482759 0.857143
28 GGS 0.482759 0.857143
29 FPQ 0.47619 0.804348
30 0FV 0.473684 0.926829
31 LA6 0.473684 0.926829
32 749 0.461538 0.871795
33 1NH 0.444444 0.787234
34 FII 0.444444 0.649123
35 SZH 0.432432 0.637931
36 PS7 0.426667 0.883721
37 9GB 0.42 0.846154
38 C0X 0.41791 0.723404
39 FHP 0.403509 0.738095
40 9AX 0.4 0.826087
Similar Ligands (3D)
Ligand no: 1; Ligand: GPP; Similar ligands found: 2
No: Ligand Similarity coefficient
1 RZ5 0.8765
2 86B 0.8716
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VG1; Ligand: FPP; 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: 2vg1.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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