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Receptor
PDB id Resolution Class Description Source Keywords
5CTW 1.48 Å EC: 5.99.1.3 CRYSTAL STRUCTURE OF THE ATP BINDING DOMAIN OF S. AUREUS GYR COMPLEXED WITH A FRAGMENT STAPHYLOCOCCUS AUREUS DNA GYRASE GYRB FRAGMENT-BASED SCREENING STRUCTURE-BASED ISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: FRAGMENT-BASED DISCOVERY OF DNA GYRASE INHIBITORS T THE ATPASE SUBUNIT OF GYRB. BIOORG.MED.CHEM.LETT. V. 26 1314 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:302;
A:302;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
MPD B:305;
B:306;
A:304;
A:305;
B:304;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
118.174 C6 H14 O2 C[C@@...
55D A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
212.269 C9 H12 N2 O2 S CCCC(...
CL A:303;
B:303;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
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 (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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....
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: 55D; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 55D 1 1
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: 208
This union binding pocket(no: 1) in the query (biounit: 3ttz.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2AGC DAO None
2 2GJ5 VD3 None
3 4TV1 36M None
4 2ALG DAO None
5 2ALG HP6 None
6 3KO0 TFP None
7 3CBC DBS 1.51515
8 1SDW IYT 1.51515
9 2F6U CIT 1.51515
10 5H2U 1N1 1.51515
11 4RF7 ARG 2.0202
12 3EFS BTN 2.0202
13 3OU2 SAH 2.0202
14 2OFV 242 2.0202
15 3EHH ADP 2.0202
16 2PNC CLU 2.52525
17 2DXU BT5 2.52525
18 2G30 ALA ALA PHE 2.52525
19 1KOR ANP 2.52525
20 1KOR ARG 2.52525
21 1KOR SIN 2.52525
22 3VPH FBP 2.52525
23 3AQT RCO 2.52525
24 4WGF HX2 2.52525
25 1WPY BTN 2.52525
26 5UXH GFB 2.52525
27 3RF4 FUN 2.58621
28 5OCG 9R5 2.6455
29 6FA4 D1W 2.89017
30 5Y3N 8MF 3.0303
31 2YBQ UP2 3.0303
32 4I3V NAD 3.0303
33 5LRT ADP 3.0303
34 4DXD 9PC 3.0303
35 2YBQ SAH 3.0303
36 2IOR ADP 3.53535
37 5XDT ZI7 3.53535
38 2XVD AS6 3.53535
39 4IPE ANP 3.53535
40 6MVU K4V 3.53535
41 5D9G GLU ASN LEU TYR PHE GLN 3.53535
42 4M0R 644 3.53535
43 5YJS SAL 3.53535
44 1BGQ RDC 4.0404
45 1F9V ADP 4.0404
46 4OYA 1VE 4.0404
47 1M5B BN1 4.0404
48 5OF1 SAL 4.0404
49 3G5N PB2 4.0404
50 5VC5 96M 4.0404
51 4L2H AR6 AR6 4.0404
52 3S5W ONH 4.0404
53 5OC1 FAD 4.0404
54 2ZL7 FUC GAL NGA 4.0404
55 4QMN DB8 4.0404
56 5LNQ CAA 4.0404
57 1QD1 FON 4.0404
58 1D7O TCL 4.0404
59 1D7O NAD 4.0404
60 2AG4 OLA 4.26829
61 2AG4 LP3 4.26829
62 5AYT L6Y 4.40252
63 1GT4 UNA 4.40252
64 5F6U 5VK 4.4586
65 6D28 NEC 4.54545
66 2O1V ADP 4.54545
67 2GFD RDA 4.54545
68 3G5D 1N1 4.54545
69 4GCZ ADP 4.54545
70 1GJW GLC 4.54545
71 4BIX ADP 4.54545
72 4P5Z Q7M 4.54545
73 5DYO FLU 4.54545
74 5L2R MLA 4.54545
75 1VA6 ADP 4.54545
76 1VA6 P2S 4.54545
77 4JDR FAD 4.54545
78 5F5R ANP 5.05051
79 4CQE CQE 5.05051
80 3LVW GSH 5.05051
81 2Z3U CRR 5.05051
82 4X3R 686 5.05051
83 3HKW IX6 5.05051
84 6H3O FAD 5.05051
85 4KBA 1QM 5.05051
86 3AB1 FAD 5.05051
87 5E58 CPZ 5.05051
88 5W4W 9WG 5.05051
89 2ART LPA AMP 5.05051
90 1WNG SAH 5.05051
91 6GNO XDI 5.18518
92 1MFI FHC 5.26316
93 2UYP PPI 5.42636
94 3R1V AZB 5.51181
95 4B7P 9UN 5.55556
96 1YC4 43P 5.55556
97 2YI0 YI0 5.55556
98 5UC4 83S 5.55556
99 3K60 ADP 5.55556
100 4LHD GLY 5.55556
101 5DQ8 FLF 5.55556
102 4WHZ 3NL 5.55556
103 4CLI 5P8 5.55556
104 2E56 MYR 5.55556
105 5H6S HDH 5.55556
106 5KJW 53C 5.55556
107 2A8X FAD 5.55556
108 3KC1 2T6 5.55556
109 4RYV ZEA 5.80645
110 5WL1 CUY 6.06061
111 5WL1 D3D 6.06061
112 4COL DTP 6.06061
113 4LOO SB4 6.06061
114 2E2R 2OH 6.06061
115 3WXL ADP 6.06061
116 4XCL AGS 6.56566
117 5G48 1FL 6.56566
118 2C2A ADP 6.56566
119 4HWS 1B3 6.56566
120 5IM3 DTP 6.56566
121 1YP1 LYS ASN LEU 6.56566
122 5D48 L96 6.57895
123 2BVE PH5 6.72269
124 3SAO DBH 6.875
125 3JU6 ANP 7.07071
126 4WOE ADP 7.07071
127 6GWR FEW 7.07071
128 5MW4 5JU 7.57576
129 3PP0 03Q 7.57576
130 4LY9 S6P 7.57576
131 1VJY 460 7.57576
132 4LY9 1YY 7.57576
133 5IXG OTP 7.69231
134 2GTF P1R 7.77778
135 5HP8 PYR 8.06452
136 4YBN FAD 8.08081
137 3AFN NAP 8.08081
138 5TUF TDC 8.58586
139 4B0T ADP 8.58586
140 5IDM ANP 8.93855
141 1RYD GLC 9.09091
142 3LL5 ADP 9.09091
143 1WKR IVA VAL VAL STA ALA STA 9.09091
144 3LL5 IPE 9.09091
145 4YRI 4JH 9.09091
146 1ECM TSA 9.17431
147 1KGI T4A 9.44882
148 5VM6 9EG 9.48905
149 4ZDM GLY 9.59596
150 4IVG ANP 9.59596
151 5VCV 1N1 9.59596
152 4TWP AXI 10.101
153 5IKH 6BW 10.101
154 5OF9 ANP 10.6061
155 3DLG GWE 11.1111
156 4MOB ADP 11.1111
157 4ZUL UN1 11.1111
158 3OJF IMJ 11.1111
159 3OJF NDP 11.1111
160 1ZNY GDP 11.6162
161 4X9X OLA 11.6162
162 2UYN 2KT 11.6279
163 2RCU BUJ 12.1212
164 3EM0 CHD 12.3188
165 1LSH PLD 12.6263
166 1RJW ETF 12.6263
167 6MPT C30 12.6263
168 3D36 ADP 13.1313
169 5FPE 3TR 13.1313
170 3H4L ANP 13.1313
171 6G0X RAM GLC GLA NAG NDG NAG 13.1313
172 1VGR COA 13.1313
173 1K97 ASP 13.6364
174 1K97 CIR 13.6364
175 6F5W KG1 13.6364
176 3QSB 743 13.6364
177 5LX9 OLB 14.1414
178 6CDO ALA VAL GLY ILE GLY ALA VAL PHE 14.6465
179 1BRW URA 14.6465
180 6H39 FGY 15.1515
181 2TPI ILE VAL 15.5172
182 4XIZ LPP 15.7143
183 1ID0 ANP 15.7895
184 5HCY 60D 16.1616
185 4L2I NAD 16.1616
186 4L2I FAD 16.1616
187 5HES 032 16.1616
188 4BG4 ADP 16.6667
189 3NZ1 3NY 17.1717
190 2P1M IHP 17.1717
191 2P1O NLA 17.1717
192 2P1O IHP 17.1717
193 5J6A P46 17.6768
194 3VRY B43 17.6768
195 1GPM AMP 17.6768
196 1PWB GLC 18.0791
197 2ZKJ ADP 18.1818
198 5OLK DTP 18.1818
199 1TH8 ADP 20
200 2XCM ADP 20.6522
201 6GMN F4E 21.1538
202 1I58 ADP 21.164
203 1I58 ACP 21.164
204 2Q8G AZX 21.2121
205 1TID ATP 21.3235
206 3CV2 COA 22.2222
207 3IHB GLU 22.7273
208 1Y8O ADP 31.8182
Pocket No.: 2; Query (leader) PDB : 3TTZ; Ligand: 07N; Similar sites found with APoc: 26
This union binding pocket(no: 2) in the query (biounit: 3ttz.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1UVC STE None
2 5A89 FMN None
3 1IZE IVA VAL VAL STA ALA STA 2.0202
4 4URF 1PS 2.0202
5 4XTX 590 2.52525
6 1FEC FAD 3.53535
7 1HXD BTN 3.53535
8 3OIG NAD 3.53535
9 1AOE NDP 3.64583
10 1AOE GW3 3.64583
11 5HWV MBN 3.84615
12 2E5A LAQ 4.0404
13 1GUZ NAD 4.54545
14 1NJR XYL 5.05051
15 1VCE SAH 5.05051
16 2GBB CIT 5.12821
17 3BBH SFG 6.06061
18 4FFG 0U8 7.07071
19 3G08 FEE 8.58586
20 5J60 FAD 8.58586
21 1Q19 SSC 9.09091
22 1KJ1 MAN 9.17431
23 1U70 NDP 10.2151
24 1U70 MTX 10.2151
25 3WV6 GAL GLC 10.6061
26 5LXT GTP 12.5874
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