Receptor
PDB id Resolution Class Description Source Keywords
5CTY 1.6 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
55H B:305;
 Valid;
 none;
 ic50 = 0.265 uM
295.319 C14 H9 N5 O S c1cc(...
MPD B:302;
A:302;
B:303;
A:301;
B:301;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
118.174 C6 H14 O2 C[C@@...
CL B:304;
A:303;
 Invalid;
Invalid;
 none;
none;
 submit data
35.453 Cl [Cl-]
MG A:304;
B:306;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
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 (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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 6KZV ic50 = 5.4 uM E0F C24 H27 N3 O2 CN(Cc1cccc....
5 6Y8O - NOV C31 H36 N2 O11 Cc1c(ccc2c....
6 4GEE Ki < 1 nM 0WT C17 H18 Cl N7 O CCc1c(c2c(....
7 4GGL Ki < 1 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
8 4HZ0 - 1AV C13 H9 N7 S c1cc(cnc1)....
9 1S14 - NOV C31 H36 N2 O11 Cc1c(ccc2c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 55H; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 55H 1 1
2 55G 0.505618 0.960784
3 57X 0.4 0.71875
Similar Ligands (3D)
Ligand no: 1; Ligand: 55H; Similar ligands found: 172
No: Ligand Similarity coefficient
1 797 0.9499
2 F33 0.9363
3 97Z 0.9336
4 9B2 0.9318
5 9AW 0.9300
6 W2E 0.9275
7 FO2 0.9269
8 S1C 0.9232
9 C9J 0.9192
10 3K1 0.9186
11 C9G 0.9169
12 L43 0.9163
13 1VG 0.9155
14 9C8 0.9140
15 DN8 0.9127
16 ZUF 0.9125
17 GA6 0.9110
18 BZH 0.9099
19 123 0.9089
20 0U7 0.9083
21 GQZ 0.9082
22 JV8 0.9057
23 31F 0.9055
24 F36 0.9053
25 Q92 0.9047
26 68Q 0.9043
27 TVC 0.9038
28 AU6 0.9038
29 FJR 0.9035
30 F5N 0.9034
31 29F 0.9033
32 BCE 0.9026
33 E8Z 0.9022
34 88S 0.9017
35 1UW 0.9013
36 32F 0.9010
37 1UT 0.9008
38 0UC 0.9006
39 72H 0.9006
40 06R 0.8999
41 AV7 0.8992
42 S16 0.8988
43 XAV 0.8983
44 F08 0.8982
45 0UA 0.8972
46 F38 0.8971
47 1UR 0.8971
48 3TH 0.8969
49 JV5 0.8967
50 Y0R 0.8964
51 MD7 0.8955
52 97K 0.8954
53 9X0 0.8943
54 O53 0.8943
55 8XY 0.8940
56 EBB 0.8940
57 KVW 0.8936
58 2ZI 0.8934
59 TFX 0.8932
60 2OX 0.8928
61 JPW 0.8924
62 Q7U 0.8924
63 9M9 0.8912
64 7B1 0.8909
65 JKN 0.8908
66 K3T 0.8907
67 QRN 0.8900
68 9EG 0.8889
69 802 0.8887
70 EEY 0.8886
71 IY5 0.8886
72 2JP 0.8876
73 100 0.8867
74 KVN 0.8866
75 JP8 0.8866
76 E98 0.8860
77 08C 0.8857
78 91F 0.8855
79 M0V 0.8850
80 FDZ 0.8849
81 KUQ 0.8844
82 T7O 0.8837
83 1V0 0.8835
84 UUL 0.8832
85 JVB 0.8832
86 135 0.8826
87 49J 0.8823
88 Z8R 0.8822
89 BZD 0.8819
90 0J6 0.8819
91 E92 0.8819
92 5ET 0.8818
93 4ZW 0.8812
94 1GV 0.8810
95 S38 0.8805
96 6MY 0.8801
97 M16 0.8799
98 80R 0.8797
99 UV4 0.8797
100 J2W 0.8796
101 KC8 0.8790
102 GBJ 0.8790
103 785 0.8789
104 A64 0.8786
105 65W 0.8784
106 0DJ 0.8774
107 36K 0.8773
108 CIU 0.8772
109 GN5 0.8772
110 TVZ 0.8771
111 9GX 0.8769
112 5XM 0.8768
113 FO5 0.8764
114 F1T 0.8760
115 7SB 0.8752
116 68C 0.8747
117 23M 0.8743
118 A63 0.8742
119 7FC 0.8741
120 361 0.8740
121 B1N 0.8731
122 J2Q 0.8728
123 KS2 0.8723
124 1UA 0.8721
125 FYE 0.8706
126 B1W 0.8703
127 1Q1 0.8702
128 F13 0.8700
129 2TH 0.8700
130 KWK 0.8698
131 1UZ 0.8697
132 ENY 0.8696
133 7GK 0.8696
134 IYX 0.8696
135 K97 0.8691
136 U1T 0.8685
137 XZ1 0.8677
138 KOT 0.8675
139 334 0.8675
140 SNP 0.8674
141 NVS 0.8671
142 2X1 0.8665
143 HTK 0.8661
144 122 0.8659
145 27F 0.8657
146 T5J 0.8648
147 NZO 0.8643
148 WF4 0.8639
149 NNF 0.8639
150 X8I 0.8635
151 82E 0.8629
152 907 0.8624
153 3G5 0.8598
154 HA1 0.8593
155 ECZ 0.8588
156 CT7 0.8588
157 1V8 0.8587
158 BMZ 0.8585
159 CR4 0.8585
160 D9Q 0.8584
161 RGZ 0.8580
162 124 0.8574
163 G2V 0.8572
164 8E3 0.8571
165 8E6 0.8559
166 F37 0.8558
167 120 0.8553
168 S06 0.8545
169 C17 0.8524
170 8EC 0.8524
171 4ZF 0.8508
172 OAQ 0.8506
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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