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Receptor
PDB id Resolution Class Description Source Keywords
4BAE 2.35 Å EC: 5.99.1.3 OPTIMISATION OF PYRROLEAMIDES AS MYCOBACTERIAL GYRB ATPASE I STRUCTURE ACTIVITY RELATIONSHIP AND IN VIVO EFFICACY IN THEM ODEL OF TUBERCULOSIS MYCOBACTERIUM SMEGMATIS ISOMERASE DNA TOPOISOMERASE INHIBITOR
Ref.: OPTIMIZATION OF PYRROLAMIDES AS MYCOBACTERIAL GYRB INHIBITORS: STRUCTURE ACTIVITY RELATIONSHIP AND IN EFFICACY IN THE MOUSE MODEL OF TUBERCULOSIS. ANTIMICROB.AGENTS CHEMOTHER. V. 58 61 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RWX C:1256;
A:1256;
B:1255;
D:1257;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 3 nM
558.837 C19 H21 Br Cl N7 O4 S Cc1c(...
GLY LYS HIS ARG VAL PHE HIS TYR PRO C:246;
B:246;
A:246;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data n/a n/a n/a n/a
CA D:1256;
D:1259;
A:1255;
C:1255;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
SO4 A:1257;
D:1258;
C:1257;
B:1256;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
GLY LYS HIS ARG VAL PHE HIS TYR PRO GLY D:246;
Part of Protein;
none;
submit data n/a n/a n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4BAE 2.35 Å EC: 5.99.1.3 OPTIMISATION OF PYRROLEAMIDES AS MYCOBACTERIAL GYRB ATPASE I STRUCTURE ACTIVITY RELATIONSHIP AND IN VIVO EFFICACY IN THEM ODEL OF TUBERCULOSIS MYCOBACTERIUM SMEGMATIS ISOMERASE DNA TOPOISOMERASE INHIBITOR
Ref.: OPTIMIZATION OF PYRROLAMIDES AS MYCOBACTERIAL GYRB INHIBITORS: STRUCTURE ACTIVITY RELATIONSHIP AND IN EFFICACY IN THE MOUSE MODEL OF TUBERCULOSIS. ANTIMICROB.AGENTS CHEMOTHER. V. 58 61 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 5D7D - 57X C17 H15 N5 O S CCCN1c2c(c....
2 5CTY ic50 = 0.265 uM 55H C14 H9 N5 O S c1cc(cnc1)....
3 5D7R ic50 = 0.013 uM 57Y C19 H16 N4 O4 S CCCc1c(ccc....
4 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
5 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
6 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
7 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
8 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
9 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
10 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
11 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
12 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
13 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
14 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
15 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
16 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
17 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
50% Homology Family (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
2 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
3 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
4 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
5 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
6 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
7 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
8 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
9 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
10 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
11 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
12 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
13 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
14 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
17 4PU9 - ADP BEF n/a n/a
18 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
22 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
23 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
24 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
25 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
26 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
27 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
28 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
29 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
30 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
31 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
32 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
33 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
34 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
35 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
36 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
37 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
38 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
39 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
40 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
41 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
42 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
43 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
44 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
45 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
46 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
47 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
48 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
49 5Z9F - AX7 C7 H7 N3 c1ccc2c(c1....
50 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RWX; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 RWX 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4BAE; Ligand: RWX; Similar sites found with APoc: 99
This union binding pocket(no: 1) in the query (biounit: 4bae.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3KO0 TFP None
2 1LNX URI None
3 2ZCQ B65 1.46341
4 3AQT RCO 1.95122
5 1IZE IVA VAL VAL STA ALA STA 1.95122
6 1XZ3 ICF 2.29885
7 5LNQ CAA 2.43902
8 3G5N PB2 2.92683
9 3OU2 SAH 2.92683
10 5O1I 9GH 2.92683
11 5X9D 80F 2.92683
12 4I5I NAD 2.92683
13 4JWK CTN 3.10881
14 5TVI O8N 3.26087
15 4GCZ ADP 3.41463
16 2C2A ADP 3.41463
17 3K60 ADP 3.41463
18 5LX9 OLB 3.41463
19 1BGQ RDC 3.90244
20 4IPE ANP 3.90244
21 4IVG ANP 3.90244
22 2F7A CCU 3.90244
23 4LHD GLY 4.39024
24 3GYT DL4 4.39024
25 5IM3 DTP 4.39024
26 6GAR FAD 4.39024
27 4WGF HX2 4.39024
28 4P7U 1PS 4.46429
29 2GBB CIT 4.48718
30 1I58 ADP 4.7619
31 1I58 ACP 4.7619
32 1GUZ NAD 4.87805
33 4UP4 GAL NAG 4.87805
34 5XJ8 NKO 4.97512
35 5HVA DUP 5
36 3L9R L9R 5.36585
37 3L9R L9Q 5.36585
38 5VLQ ANP 5.36585
39 1NJR XYL 5.36585
40 3FSM 2NC 5.41872
41 1GKZ ADP 5.85366
42 6GAS FAD 5.85366
43 1TID ATP 5.88235
44 4XCL AGS 6.34146
45 2IOR ADP 6.34146
46 4GID 0GH 6.34146
47 1XHL TNE 6.34146
48 4XQC NAD 6.34146
49 4XQC 13D 6.34146
50 1GJW GLC 6.82927
51 3IHB GLU 6.82927
52 1YP1 LYS ASN LEU 6.93069
53 3KC1 2T6 7.12166
54 1WDK NAD 7.31707
55 4GAA BES 7.31707
56 1TH8 ADP 7.58621
57 1Q19 APC 7.80488
58 5IDM ANP 7.82123
59 3KP6 SAL 7.94702
60 5IXG OTP 8.28402
61 2Y7P SAL 8.29268
62 3SM2 478 9.09091
63 4NJS G08 9.09091
64 2WG9 OCA 9.23077
65 1I7M PUT 9.26829
66 3DZ6 PUT 9.26829
67 3EHH ADP 9.26829
68 6D28 NEC 9.7561
69 2GFD RDA 9.7561
70 2O1V ADP 9.7561
71 1BZY IMU 9.7561
72 1WKR IVA VAL VAL STA ALA STA 10.7317
73 4B7P 9UN 11.2195
74 1YC4 43P 11.2195
75 2YI0 YI0 11.2195
76 3H4L ANP 11.2195
77 4L2I FAD 11.7073
78 4L2I NAD 11.7073
79 4YHQ G10 12.1212
80 2FXD DR7 12.1212
81 5OF9 ANP 12.1951
82 4WZ8 3W7 12.1951
83 5UC4 83S 12.2727
84 1ID0 ANP 12.5
85 5IXK 6EW 13.1707
86 1Y8O ADP 13.6585
87 4BIX ADP 13.6585
88 5J6A P46 14.1463
89 2ZKJ ADP 14.1463
90 2XCM ADP 14.8649
91 3EHG ATP 15.625
92 5F5R ANP 16.5854
93 5Y3N 8MF 16.5854
94 3D36 ADP 18.0488
95 2Q8G AZX 19.5122
96 4ZUL UN1 19.5122
97 5AOG IAC 24.3902
98 1B63 ANP 33.1707
99 1N4H REA 33.3333
Pocket No.: 2; Query (leader) PDB : 4BAE; Ligand: RWX; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 4bae.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZUY TCH 2.16718
2 4RHP PEF 2.92683
3 5O3Q CMP 3.33333
4 1RL4 BRR 3.7234
5 3O01 DXC 3.90244
6 5IUY BOG 3.90244
7 1G27 BB1 7.7381
8 2P3C 3TL 10.101
9 4WO4 JLS 12
Pocket No.: 3; Query (leader) PDB : 4BAE; Ligand: RWX; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 4bae.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3DJF BC3 6.34146
2 1ZAP A70 11.7073
3 1IDA 0PO 16.1616
Pocket No.: 4; Query (leader) PDB : 4BAE; Ligand: RWX; Similar sites found with APoc: 4
This union binding pocket(no: 4) in the query (biounit: 4bae.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2Q7D ANP 2.43902
2 3GKJ HC3 3.90244
3 3KA2 2NC 5.41872
4 3GGU 017 7.07071
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