Receptor
PDB id Resolution Class Description Source Keywords
6CCQ 1.92 Å EC: 2.7.7.3 CRYSTAL STRUCTURE OF E.COLI PHOSPHOPANTETHEINE ADENYLYLTRANS (PPAT/COAD) IN COMPLEX WITH 2-(3-CHLOROPHENETHYL)-1H- B ENZO[D]IMIDAZOL-4-OL ESCHERICHIA COLI (STRAIN K12) PPAT COAD FBDD PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE GRAM-NANTIBACTERIAL ANTIBIOTIC TRANSFERASE-ANTIBIOTIC COMPLEX
Ref.: FRAGMENT-BASED DRUG DISCOVERY OF INHIBITORS OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE FROM GRAM-NE BACTERIA. J. MED. CHEM. V. 61 3309 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:205;
B:202;
A:202;
A:204;
A:203;
B:203;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
EX7 B:201;
A:201;
 Valid;
Valid;
 none;
none;
 ic50 = 0.25 uM
272.73 C15 H13 Cl N2 O c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6CHP 1.94 Å EC: 2.7.7.3 PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE (COAD) IN COMPLEX WIT (R)-4-(3-(2-CYANO-1-((5-METHYL-1H-IMIDAZO[4,5-B]PYRIDIN-2-YE THYL)BENZYL)PIPERIDINE-1-CARBOXYLATE ESCHERICHIA COLI (STRAIN K12) DEPHOSPHO-COA PYROPHOSPHORYLASE PANTETHEINE-PHOSPHATE ADENYLYLTRANSFERASE PPAT CAAD FBDD GRAM-NEGATI PANTETHEINEPHOSPHATE ADENYLYLTRANSFERASEVE ANTIBACTERIAL ANTIBIOTIC TRANSFERASE TRANSFERASE-ANTIBIOTIC COMPLEX TRANSFERASE-ANTCOMPLEX
Ref.: DISCOVERY AND OPTIMIZATION OF PHOSPHOPANTETHEINE ADENYLYLTRANSFERASE INHIBITORS WITH GRAM-NEGATIVE ANTIBACTERIAL ACTIVITY. J. MED. CHEM. V. 61 3325 2018
Members (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 6CHO ic50 = 167 nM F14 C21 H21 N5 O3 CC1=Nc2nc(....
2 6CHL Kd = 9 nM EXJ C15 H13 Cl N6 O CC1=Nc2nc(....
3 6CCN ic50 = 30 uM EXS C15 H21 N3 O4 CC(C)(CO)[....
4 6CCM ic50 = 5.6 uM EXP C13 H12 Br N5 O CC1=Nc2nc(....
5 6CHN Kd = 11 nM F1D C22 H25 N7 O4 CC1=Nc2nc(....
6 6B7C Kd = 7.2 uM CWP C13 H16 N6 Cc1ccc2c(n....
7 6B7A Kd = 32 uM CWM C8 H8 N2 O Cc1[nH]c2c....
8 6CCL ic50 = 273 uM EXG C13 H11 N3 c1ccc(cc1)....
9 1H1T - PNS C11 H23 N2 O7 P S CC(C)(COP(....
10 1GN8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 6CCK ic50 = 0.037 uM EXJ C15 H13 Cl N6 O CC1=Nc2nc(....
12 1B6T - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
13 6CHQ ic50 = 4.4 uM F0V C20 H19 Cl N5 Cc1ccc(cc1....
14 6CCQ ic50 = 0.25 uM EX7 C15 H13 Cl N2 O c1cc(cc(c1....
15 6CHP Kd = 0.075 nM F0Y C24 H28 N6 O2 Cc1ccc2c(n....
16 6CCS ic50 = 230 uM EXD C8 H5 F3 N2 O c1cc2c(c(c....
17 6CKW Kd = 0.83 nM F6D C24 H25 Cl N8 O Cc1cc(n2c(....
18 6B7D Kd = 52 uM CWG C13 H13 Cl N2 O Cc1c(c(nnc....
19 6CCO ic50 = 0.051 uM EXV C19 H18 N2 O3 c1cc(cc(c1....
20 6B7B Kd = 1280 uM CWJ C10 H11 N O Cc1cc2cc(c....
21 1QJC - PNS C11 H23 N2 O7 P S CC(C)(COP(....
22 6CHM ic50 = 199 uM F1V C16 H22 N2 O2 CC(C)(C)C(....
23 6B7E Kd = 28 uM CWA C15 H14 F2 N2 O2 CC1([C@@H]....
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 6CHO ic50 = 167 nM F14 C21 H21 N5 O3 CC1=Nc2nc(....
2 6CHL Kd = 9 nM EXJ C15 H13 Cl N6 O CC1=Nc2nc(....
3 6CCN ic50 = 30 uM EXS C15 H21 N3 O4 CC(C)(CO)[....
4 6CCM ic50 = 5.6 uM EXP C13 H12 Br N5 O CC1=Nc2nc(....
5 6CHN Kd = 11 nM F1D C22 H25 N7 O4 CC1=Nc2nc(....
6 6B7C Kd = 7.2 uM CWP C13 H16 N6 Cc1ccc2c(n....
7 6B7A Kd = 32 uM CWM C8 H8 N2 O Cc1[nH]c2c....
8 6CCL ic50 = 273 uM EXG C13 H11 N3 c1ccc(cc1)....
9 1H1T - PNS C11 H23 N2 O7 P S CC(C)(COP(....
10 1GN8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 6CCK ic50 = 0.037 uM EXJ C15 H13 Cl N6 O CC1=Nc2nc(....
12 1B6T - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
13 6CHQ ic50 = 4.4 uM F0V C20 H19 Cl N5 Cc1ccc(cc1....
14 6CCQ ic50 = 0.25 uM EX7 C15 H13 Cl N2 O c1cc(cc(c1....
15 6CHP Kd = 0.075 nM F0Y C24 H28 N6 O2 Cc1ccc2c(n....
16 6CCS ic50 = 230 uM EXD C8 H5 F3 N2 O c1cc2c(c(c....
17 6CKW Kd = 0.83 nM F6D C24 H25 Cl N8 O Cc1cc(n2c(....
18 6B7D Kd = 52 uM CWG C13 H13 Cl N2 O Cc1c(c(nnc....
19 6CCO ic50 = 0.051 uM EXV C19 H18 N2 O3 c1cc(cc(c1....
20 6B7B Kd = 1280 uM CWJ C10 H11 N O Cc1cc2cc(c....
21 1QJC - PNS C11 H23 N2 O7 P S CC(C)(COP(....
22 6CHM ic50 = 199 uM F1V C16 H22 N2 O2 CC(C)(C)C(....
23 6B7E Kd = 28 uM CWA C15 H14 F2 N2 O2 CC1([C@@H]....
24 3UC5 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
25 1OD6 - PNS C11 H23 N2 O7 P S CC(C)(COP(....
26 5O0H - 9FN C14 H8 Cl N O5 c1ccc(c(c1....
27 4NAT - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
28 4RUK - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
29 3X1J Ki = 8.4 uM ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
30 3X1M Ki = 6.5 uM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6CHO ic50 = 167 nM F14 C21 H21 N5 O3 CC1=Nc2nc(....
2 6CHL Kd = 9 nM EXJ C15 H13 Cl N6 O CC1=Nc2nc(....
3 6CCN ic50 = 30 uM EXS C15 H21 N3 O4 CC(C)(CO)[....
4 6CCM ic50 = 5.6 uM EXP C13 H12 Br N5 O CC1=Nc2nc(....
5 6CHN Kd = 11 nM F1D C22 H25 N7 O4 CC1=Nc2nc(....
6 6B7C Kd = 7.2 uM CWP C13 H16 N6 Cc1ccc2c(n....
7 6B7A Kd = 32 uM CWM C8 H8 N2 O Cc1[nH]c2c....
8 6CCL ic50 = 273 uM EXG C13 H11 N3 c1ccc(cc1)....
9 1H1T - PNS C11 H23 N2 O7 P S CC(C)(COP(....
10 1GN8 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 6CCK ic50 = 0.037 uM EXJ C15 H13 Cl N6 O CC1=Nc2nc(....
12 1B6T - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
13 6CHQ ic50 = 4.4 uM F0V C20 H19 Cl N5 Cc1ccc(cc1....
14 6CCQ ic50 = 0.25 uM EX7 C15 H13 Cl N2 O c1cc(cc(c1....
15 6CHP Kd = 0.075 nM F0Y C24 H28 N6 O2 Cc1ccc2c(n....
16 6CCS ic50 = 230 uM EXD C8 H5 F3 N2 O c1cc2c(c(c....
17 6CKW Kd = 0.83 nM F6D C24 H25 Cl N8 O Cc1cc(n2c(....
18 6B7D Kd = 52 uM CWG C13 H13 Cl N2 O Cc1c(c(nnc....
19 6CCO ic50 = 0.051 uM EXV C19 H18 N2 O3 c1cc(cc(c1....
20 6B7B Kd = 1280 uM CWJ C10 H11 N O Cc1cc2cc(c....
21 1QJC - PNS C11 H23 N2 O7 P S CC(C)(COP(....
22 6CHM ic50 = 199 uM F1V C16 H22 N2 O2 CC(C)(C)C(....
23 6B7E Kd = 28 uM CWA C15 H14 F2 N2 O2 CC1([C@@H]....
24 3ND7 - PNY C11 H22 N2 O4 S CC(C)(CO)[....
25 3ND6 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
26 3UC5 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
27 3PNB - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
28 3NBK - PNS C11 H23 N2 O7 P S CC(C)(COP(....
29 1OD6 - PNS C11 H23 N2 O7 P S CC(C)(COP(....
30 5O0A Kd = 0.58 mM 9FH C11 H10 N2 O2 Cc1c(cnn1c....
31 5O0D - 9F5 C14 H12 O4 c1ccc(cc1)....
32 5O0F - IOP C11 H11 N O2 c1ccc2c(c1....
33 5O08 - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
34 5O0C - 9F8 C12 H13 N O2 Cc1cn(c2c1....
35 5O0B Kd = 66 uM 9FE C8 H5 Br N2 O2 c1cc2c(cc1....
36 5O0H - 9FN C14 H8 Cl N O5 c1ccc(c(c1....
37 3K9W - ADE C5 H5 N5 c1[nH]c2c(....
38 3PXU - COD C21 H35 N7 O13 P2 S CC(C)(CO[P....
39 1O6B - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
40 4NAU - 2W3 C25 H26 Cl2 N6 O4 CCc1cc(nc(....
41 4NAH - 2VJ C24 H25 Cl2 N5 O3 S CCc1cc(nc(....
42 3F3M - PPS C10 H15 N5 O13 P2 S c1nc(c2c(n....
43 4NAT - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 4RUK - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
45 3X1J Ki = 8.4 uM ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
46 3X1M Ki = 6.5 uM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
47 1VLH - PNS C11 H23 N2 O7 P S CC(C)(COP(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: EX7; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 EX7 1 1
2 CWM 0.40678 0.714286
Similar Ligands (3D)
Ligand no: 1; Ligand: EX7; Similar ligands found: 81
No: Ligand Similarity coefficient
1 EXP 0.9785
2 5RU 0.9520
3 CWP 0.9420
4 6IP 0.9401
5 IW4 0.9369
6 5RW 0.9305
7 5RX 0.9260
8 A06 0.9252
9 LJ2 0.9232
10 5RV 0.9230
11 F91 0.9219
12 IW5 0.9167
13 1UA 0.9143
14 L12 0.9137
15 OA5 0.9137
16 DIH 0.9094
17 IW3 0.9085
18 IM5 0.9074
19 C0V 0.9034
20 1PB 0.9029
21 AX6 0.9015
22 HPK 0.9014
23 RNK 0.8986
24 SE5 0.8971
25 YKN 0.8951
26 5RZ 0.8949
27 STS 0.8939
28 1A6 0.8932
29 O2Q 0.8929
30 3BE 0.8926
31 1Q2 0.8906
32 A6E 0.8905
33 QNI 0.8903
34 LJ1 0.8901
35 SZA 0.8894
36 QDR 0.8893
37 IDE 0.8892
38 YH2 0.8892
39 BXS 0.8880
40 WDT 0.8861
41 N18 0.8855
42 0OM 0.8846
43 M62 0.8845
44 28C 0.8841
45 EBB 0.8836
46 OX3 0.8833
47 P1J 0.8817
48 0QX 0.8816
49 IEE 0.8806
50 BZM 0.8804
51 1OX 0.8802
52 PGI 0.8791
53 7WD 0.8775
54 9RK 0.8775
55 0RU 0.8774
56 NHV 0.8770
57 49G 0.8762
58 4KN 0.8758
59 7BW 0.8742
60 35K 0.8704
61 0QR 0.8695
62 49Z 0.8694
63 MH5 0.8692
64 0QA 0.8683
65 ZW2 0.8672
66 3D3 0.8665
67 BDE 0.8665
68 CKH 0.8665
69 G8V 0.8654
70 GYZ 0.8648
71 62P 0.8647
72 9PC 0.8645
73 P9L 0.8631
74 4BE 0.8627
75 1Q1 0.8626
76 B2K 0.8598
77 38D 0.8596
78 2BE 0.8595
79 0OP 0.8568
80 GB7 0.8554
81 MF5 0.8520
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6CHP; Ligand: F0Y; 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: 6chp.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6CHP; Ligand: F0Y; 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: 6chp.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6CHP; Ligand: F0Y; 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: 6chp.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6CHP; Ligand: F0Y; 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: 6chp.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6CHP; Ligand: F0Y; 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: 6chp.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6CHP; Ligand: F0Y; 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: 6chp.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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