Receptor
PDB id Resolution Class Description Source Keywords
5d6p 2.05 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF THE ATP BINDING DOMAIN OF S. AUREUS GYR COMPLEXED WITH A LIGAND STAPHYLOCOCCUS AUREUS DNA GYRASE GYRB LIGAND STRUCTURE-BASED DESIGN ISOMERASE-INHIBITOR COMPLEX
Ref.: DISCOVERY OF AZAINDOLE UREAS AS A NOVEL CLASS OF BA GYRASE B INHIBITORS. J.MED.CHEM. V. 58 8503 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MPD B:302;
A:302;
B:303;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
118.174 C6 H14 O2 C[C@@...
GOL A:303;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
57U A:301;
B:301;
 Valid;
Valid;
 none;
none;
 ic50 = 2.5 uM
266.319 C11 H14 N4 O2 S CCNC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3TTZ 1.63 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF A TOPOISOMERASE ATPASE INHIBITOR STAPHYLOCOCCUS AUREUS PROTEIN-INHIBITOR COMPLEX ATP-BINDING STRUCTURE-BASED DRUGANTIMICROBIAL ISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: PYRROLAMIDE DNA GYRASE INHIBITORS: OPTIMIZATION OF ANTIBACTERIAL ACTIVITY AND EFFICACY. BIOORG.MED.CHEM.LETT. V. 21 7416 2011
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 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 6TCK - N1N C21 H15 Cl2 N3 O4 S Cc1c(c(c([....
15 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 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 6TCK - N1N C21 H15 Cl2 N3 O4 S Cc1c(c(c([....
15 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
16 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
17 6Y8N ic50 = 9 nM OGH C21 H21 F N8 O Cc1ncc(cn1....
18 6Y8L - NOV C31 H36 N2 O11 Cc1c(ccc2c....
19 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
20 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
50% Homology Family (67)
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 6TCK - N1N C21 H15 Cl2 N3 O4 S Cc1c(c(c([....
13 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
14 6YD9 ic50 = 110 nM ON2 C16 H15 Cl2 N5 O2 S Cc1c(c(c([....
15 6F94 ic50 = 0.099 uM D0H C23 H25 N5 O2 CCNC(=O)Nc....
16 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
17 6KZX ic50 = 0.2 uM E0L C18 H15 N3 O4 CNc1cccc2c....
18 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
19 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
20 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
21 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
22 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
23 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
24 6KZZ ic50 = 0.0017 uM E0R C18 H15 N3 O4 CNc1cccc2c....
25 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
26 6F86 ic50 = 0.037 uM CWW C17 H16 Br N7 O2 CCNC(=O)Nc....
27 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
28 6F8J ic50 = 0.086 uM CZ5 C17 H17 N7 O2 CCNC(=O)Nc....
29 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
30 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
31 7C7O ic50 = 0.52 nM FKU C21 H22 F N5 O4 CNc1cc(cc2....
32 7C7N ic50 = 0.36 nM FKR C18 H14 F N3 O4 CNc1cc(cc2....
33 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
34 6F96 ic50 = 0.019 uM D0K C21 H22 N6 O3 CCNC(=O)Nc....
35 5Z9F - AX7 C7 H7 N3 c1ccc2c(c1....
36 6ENH - BHW C55 H59 N5 O20 Cc1ccc([nH....
37 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
38 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
39 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
40 6ENG - BHW C55 H59 N5 O20 Cc1ccc([nH....
41 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
42 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
43 4PU9 - ADP BEF n/a n/a
44 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
45 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
46 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
47 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
48 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
49 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
50 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
51 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
52 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
53 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
54 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
55 6Y8N ic50 = 9 nM OGH C21 H21 F N8 O Cc1ncc(cn1....
56 6Y8L - NOV C31 H36 N2 O11 Cc1c(ccc2c....
57 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
58 4LP0 ic50 < 10 nM 1YM C18 H14 F3 N5 O3 S CCNC(=O)Nc....
59 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
60 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
61 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
62 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
63 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
64 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
65 6M1S Ki < 1 nM EZ9 C26 H23 F4 N7 O3 CCNc1cc(cc....
66 6M1J Ki = 2 nM EZ6 C24 H17 F4 N7 O2 CNc1cc(cc2....
67 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 57U; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 57U 1 1
2 57V 0.487805 0.821429
Similar Ligands (3D)
Ligand no: 1; Ligand: 57U; Similar ligands found: 154
No: Ligand Similarity coefficient
1 27F 0.9277
2 1UZ 0.9233
3 A64 0.9165
4 4UM 0.9108
5 A63 0.9106
6 A73 0.9088
7 91F 0.9062
8 1V1 0.9053
9 20D 0.9052
10 DFL 0.9046
11 1FE 0.9031
12 3TI 0.9029
13 08C 0.9021
14 25F 0.9019
15 5WW 0.9014
16 O53 0.9000
17 NKI 0.8999
18 P83 0.8986
19 1UR 0.8978
20 1V0 0.8977
21 F36 0.8967
22 DFV 0.8948
23 29F 0.8945
24 RGK 0.8933
25 0RY 0.8930
26 WLH 0.8928
27 RF2 0.8926
28 SZ5 0.8920
29 2UV 0.8920
30 NU3 0.8918
31 GN5 0.8911
32 06R 0.8911
33 W2E 0.8905
34 O82 0.8898
35 3F4 0.8893
36 SNJ 0.8893
37 IK1 0.8893
38 AGI 0.8891
39 1UT 0.8889
40 NAR 0.8877
41 UN9 0.8874
42 9XZ 0.8857
43 FX5 0.8852
44 EY2 0.8848
45 O9T 0.8847
46 TVZ 0.8847
47 ZEA 0.8845
48 ROL 0.8839
49 AO 0.8836
50 HRD 0.8834
51 O9Z 0.8826
52 U4J 0.8820
53 6JP 0.8818
54 SNP 0.8809
55 5KN 0.8807
56 B7H 0.8801
57 F08 0.8793
58 1V4 0.8793
59 31F 0.8792
60 HPX 0.8789
61 KMP 0.8785
62 H2W 0.8780
63 E9L 0.8779
64 CDJ 0.8778
65 6DH 0.8778
66 R4E 0.8777
67 W8L 0.8773
68 SAK 0.8773
69 62D 0.8772
70 OAQ 0.8770
71 M3W 0.8769
72 XAV 0.8768
73 LC1 0.8767
74 IPJ 0.8761
75 HH6 0.8751
76 GVI 0.8749
77 FZ0 0.8748
78 N5B 0.8744
79 1VG 0.8744
80 1V8 0.8743
81 C0V 0.8742
82 P34 0.8737
83 S98 0.8735
84 MRE 0.8725
85 LZ7 0.8721
86 8XT 0.8721
87 1V3 0.8719
88 20N 0.8712
89 36I 0.8709
90 NFZ 0.8708
91 2WU 0.8704
92 97K 0.8699
93 VT3 0.8699
94 M16 0.8695
95 1UW 0.8695
96 FSE 0.8695
97 4AU 0.8695
98 6BK 0.8694
99 338 0.8692
100 S1C 0.8686
101 A9E 0.8680
102 1R5 0.8676
103 ML1 0.8671
104 IY5 0.8658
105 CLI 0.8654
106 01I 0.8653
107 F40 0.8649
108 L43 0.8649
109 DDC 0.8649
110 7FC 0.8647
111 FDZ 0.8643
112 517 0.8642
113 CWE 0.8642
114 YE6 0.8641
115 VFJ 0.8635
116 Q7U 0.8633
117 KU1 0.8629
118 RNP 0.8626
119 AXX 0.8625
120 LLG 0.8623
121 HCC 0.8620
122 EEY 0.8618
123 1HP 0.8618
124 2ZI 0.8615
125 LU2 0.8610
126 3WL 0.8610
127 6JM 0.8606
128 YEX 0.8605
129 DN8 0.8604
130 FNT 0.8603
131 X2L 0.8601
132 GA6 0.8600
133 AJ1 0.8599
134 272 0.8597
135 N4N 0.8595
136 A8D 0.8593
137 6T5 0.8592
138 2GQ 0.8579
139 6TJ 0.8575
140 90G 0.8575
141 T5J 0.8572
142 SGW 0.8571
143 JTF 0.8570
144 7G2 0.8561
145 CMG 0.8560
146 ASE 0.8556
147 BBP 0.8554
148 MXM 0.8550
149 QUE 0.8542
150 CFK 0.8533
151 0K7 0.8532
152 4HG 0.8525
153 LI7 0.8521
154 5WT 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3TTZ; Ligand: 07N; 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: 3ttz.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3TTZ; Ligand: 07N; 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: 3ttz.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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