Receptor
PDB id Resolution Class Description Source Keywords
4Q9M 2.06 Å EC: 2.5.1.- CRYSTAL STRUCTURE OF UPPS IN COMPLEX WITH FPP AND AN ALLOSTE INHIBITOR STREPTOCOCCUS PNEUMONIAE UNDECAPRENYL DIPHOSPHATE SYNTHASE TRANSFERASE-TRANSFERASE ICOMPLEX
Ref.: DISCOVERY AND STRUCTURAL CHARACTERIZATION OF AN ALL INHIBITOR OF BACTERIAL CIS-PRENYLTRANSFERASE. PROTEIN SCI. V. 24 20 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CD B:305;
A:306;
B:303;
A:303;
A:304;
A:311;
B:307;
B:306;
A:309;
A:308;
A:305;
B:304;
A:310;
A:307;
B:308;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
112.411 Cd [Cd+2...
2ZW A:301;
B:301;
Valid;
Valid;
none;
none;
Kd = 66 nM
354.83 C20 H19 Cl N2 O2 Cc1c(...
FPP A:302;
B:302;
Valid;
Valid;
none;
none;
submit data
382.326 C15 H28 O7 P2 CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4Q9M 2.06 Å EC: 2.5.1.- CRYSTAL STRUCTURE OF UPPS IN COMPLEX WITH FPP AND AN ALLOSTE INHIBITOR STREPTOCOCCUS PNEUMONIAE UNDECAPRENYL DIPHOSPHATE SYNTHASE TRANSFERASE-TRANSFERASE ICOMPLEX
Ref.: DISCOVERY AND STRUCTURAL CHARACTERIZATION OF AN ALL INHIBITOR OF BACTERIAL CIS-PRENYLTRANSFERASE. PROTEIN SCI. V. 24 20 2015
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
2 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
2 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 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 = 7.5 uM 53Q C21 H17 Cl O COc1ccc(cc....
5 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
6 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
7 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
8 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
9 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
11 3WYJ ic50 = 1.9 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
12 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
13 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
14 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
15 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
16 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
17 5HC7 - DST C5 H14 O6 P2 S CC(C)CCS[P....
18 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
19 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
20 4U82 ic50 = 0.39 uM FPS C15 H28 O6 P2 S CC(=CCC/C(....
21 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
22 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2ZW; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 2ZW 1 1
2 1U3 0.554054 0.688525
Ligand no: 2; Ligand: FPP; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 OTP 1 0.975
2 ZTP 1 0.975
3 GRG 1 1
4 FPP 1 1
5 VTP 1 0.975
6 GPP 0.911111 0.974359
7 DSL 0.744681 0.9
8 0K3 0.744681 0.9
9 FJP 0.744681 0.923077
10 FDF 0.727273 0.904762
11 FFF 0.714286 0.928571
12 FGG 0.590164 0.928571
13 FPF 0.57377 0.928571
14 2CF 0.57377 0.928571
15 10E 0.568627 0.702128
16 10D 0.568627 0.785714
17 MGM 0.5625 0.764706
18 DMA 0.5625 0.846154
19 A4S 0.558824 0.698113
20 3E9 0.555556 0.951219
21 FPS 0.551724 0.880952
22 GGS 0.551724 0.880952
23 H6P 0.54902 0.785714
24 FPQ 0.539683 0.826087
25 10G 0.538462 0.767442
26 FII 0.507937 0.666667
27 GST 0.482759 0.857143
28 PS7 0.48 0.906977
29 FHP 0.473684 0.761905
30 1NH 0.457831 0.770833
31 0FV 0.442623 0.904762
32 LA6 0.442623 0.904762
33 749 0.428571 0.897436
34 SZH 0.428571 0.655172
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4Q9M; Ligand: FPP; Similar sites found: 21
This union binding pocket(no: 1) in the query (biounit: 4q9m.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F4S EFO 0.01532 0.42867 None
2 3WBG 2AN 0.01335 0.41198 None
3 1FK5 OLA 0.01089 0.40057 None
4 1H0A I3P 0.03212 0.41366 1.26582
5 1RL4 BL5 0.007047 0.41374 1.59574
6 5ENZ UDP 0.01752 0.40311 1.62602
7 3W54 RNB 0.02687 0.40063 2.03252
8 2J5V PCA 0.01112 0.45814 2.43902
9 1TV5 A26 0.03625 0.40089 2.84553
10 3CV2 COA 0.04667 0.40713 3.65854
11 1DQE BOM 0.01118 0.40588 5.10949
12 3KU0 ADE 0.03719 0.40884 5.69106
13 3UUA 0CZ 0.02147 0.41262 6.09756
14 3TL1 JRO 0.03259 0.41098 6.91824
15 4H69 10Y 0.02556 0.40169 8.24742
16 1J78 VDY 0.02529 0.41281 9.34959
17 2YOO K2B 0.01123 0.40889 9.34959
18 5DCH 1YO 0.0413 0.40686 9.89583
19 2Y69 CHD 0.03201 0.41221 12.1622
20 1NSA BEN 0.0359 0.40187 14.2276
21 1VJ7 GPX 0.01911 0.42515 15.4472
Pocket No.: 2; Query (leader) PDB : 4Q9M; Ligand: 2ZW; 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: 4q9m.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4Q9M; Ligand: 2ZW; Similar sites found: 21
This union binding pocket(no: 3) in the query (biounit: 4q9m.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F4S EFO 0.00811 0.42739 None
2 3WBG 2AN 0.009709 0.40265 None
3 4OIV XX9 0.01682 0.40424 2.21239
4 1TV5 N8E 0.02747 0.40013 2.84553
5 1Z8O DEB 0.00666 0.40935 3.25203
6 4H6B 10X 0.01373 0.41118 3.58974
7 1M2W MTL 0.01155 0.41951 3.65854
8 3KRR DQX 0.04087 0.40117 4.06504
9 3G5D 1N1 0.02959 0.4005 4.06504
10 1EWF PC1 0.02074 0.401 4.47154
11 2H7C COA 0.02493 0.40971 4.87805
12 1OUK 084 0.03775 0.418 5.28455
13 3KU0 ADE 0.02055 0.40884 5.69106
14 3MDV CL6 0.005896 0.41832 6.50407
15 5CSD ACD 0.009714 0.41517 7.54717
16 1HYH NAD 0.008833 0.40925 8.13008
17 4CDN FO1 0.02284 0.40582 8.53659
18 5DCH 1YO 0.02213 0.40686 9.89583
19 2Y69 CHD 0.02243 0.40122 12.1622
20 1VJ7 GPX 0.01043 0.42515 15.4472
21 5EW9 5VC 0.01859 0.43372 15.8537
Pocket No.: 4; Query (leader) PDB : 4Q9M; Ligand: FPP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4q9m.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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