Receptor
PDB id Resolution Class Description Source Keywords
3HYF 1.7 Å EC: 3.4.23.16 CRYSTAL STRUCTURE OF HIV-1 RNASE H P15 WITH ENGINEERED E. CO AND ACTIVE SITE INHIBITOR HUMAN IMMUNODEFICIENCY VIRUS 1, ESCHERCOLI RNASE H HIV-1 HYDROLASE DI-VALENT METAL NUCLEIC ACID CLEAMECHANISM DI-VALENT METAL COORDINATION ASPARTYL PROTEASEINTEGRATION DNA RECOMBINATION ENDONUCLEASE MULTIFUNCTIONENZYME NUCLEASE NUCLEOTIDYLTRANSFERASE PROTEASE RNA-DIRPOLYMERASE TRANSFERASE MAGNESIUM METAL-BINDING
Ref.: RNASE H ACTIVE SITE INHIBITORS OF HUMAN IMMUNODEFIC VIRUS TYPE 1 REVERSE TRANSCRIPTASE: DESIGN, BIOCHEM ACTIVITY, AND STRUCTURAL INFORMATION. J.MED.CHEM. V. 52 5781 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:650;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
GOL A:698;
A:699;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
MN A:601;
A:602;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
54.938 Mn [Mn+2...
ON1 A:701;
 Valid;
 none;
 ic50 = 1.2 uM
315.109 C12 H8 Cl2 N2 O4 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3QIN 1.7 Å EC: 3.4.23.16 CRYSTAL STRUCTURE OF HIV-1 RNASE H P15 WITH ENGINEERED E. CO AND PYRIMIDINOL CARBOXYLIC ACID INHIBITOR HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GRSUBTYPE B, ESCHERICHIA COLI (STRAIN K12), HUMAN IMMUNODEFICVIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE HXB2) RNASE H HIV-1 INHIBITOR NUCLEASE TRANSFERASE HYDROLASE-COMPLEX
Ref.: STRUCTURAL AND BINDING ANALYSIS OF PYRIMIDINOL CARB ACID AND N-HYDROXY QUINAZOLINEDIONE HIV-1 RNASE H INHIBITORS. ANTIMICROB.AGENTS CHEMOTHER. V. 55 2905 2011
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 3QIN Kd = 136 nM P1Y C13 H11 Br N2 O5 COc1ccc(cc....
2 3HYF ic50 = 1.2 uM ON1 C12 H8 Cl2 N2 O4 c1cc(c(cc1....
3 3QIO Kd = 144 nM QID C14 H10 N2 O5 S c1ccc(cc1)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3QIN Kd = 136 nM P1Y C13 H11 Br N2 O5 COc1ccc(cc....
2 3HYF ic50 = 1.2 uM ON1 C12 H8 Cl2 N2 O4 c1cc(c(cc1....
3 3QIO Kd = 144 nM QID C14 H10 N2 O5 S c1ccc(cc1)....
4 3K2P Kd = 6 uM JTH C10 H12 O3 CC(C)C1=CC....
5 4QAG ic50 = 4.8 uM F95 C11 H8 O6 c1cc(c(c2c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3QIN Kd = 136 nM P1Y C13 H11 Br N2 O5 COc1ccc(cc....
2 3HYF ic50 = 1.2 uM ON1 C12 H8 Cl2 N2 O4 c1cc(c(cc1....
3 3QIO Kd = 144 nM QID C14 H10 N2 O5 S c1ccc(cc1)....
4 3K2P Kd = 6 uM JTH C10 H12 O3 CC(C)C1=CC....
5 4QAG ic50 = 4.8 uM F95 C11 H8 O6 c1cc(c(c2c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ON1; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 ON1 1 1
2 P1Y 0.560606 0.907407
Similar Ligands (3D)
Ligand no: 1; Ligand: ON1; Similar ligands found: 129
No: Ligand Similarity coefficient
1 TCW 0.9394
2 AX8 0.9359
3 QC1 0.9339
4 4P8 0.9268
5 LVE 0.9192
6 4VT 0.9187
7 N1Y 0.9185
8 94M 0.9155
9 TOP 0.9144
10 LI4 0.9134
11 12R 0.9130
12 AUY 0.9128
13 BC3 0.9114
14 IM4 0.9100
15 I0D 0.9100
16 50Q 0.9078
17 F0C 0.9068
18 3AK 0.9060
19 AHR AHR 0.9056
20 AX4 0.9049
21 FVY 0.9044
22 7WD 0.9044
23 RK4 0.9026
24 EMU 0.9023
25 5AV 0.9009
26 AEY 0.9008
27 D5F 0.9008
28 9ME 0.9000
29 MH5 0.8998
30 531 0.8996
31 IWH 0.8995
32 SCE 0.8994
33 0QX 0.8974
34 F91 0.8968
35 GLA GAL 0.8955
36 KTV 0.8949
37 9FN 0.8948
38 KUP 0.8941
39 XDH 0.8935
40 JCQ 0.8933
41 A4V 0.8931
42 0RU 0.8928
43 TH4 0.8927
44 HHV 0.8919
45 S0I 0.8917
46 8MF 0.8908
47 5OU 0.8894
48 DE7 0.8892
49 EDG AHR 0.8891
50 R75 0.8888
51 M01 0.8886
52 NIP 0.8879
53 NOJ BGC 0.8877
54 M62 0.8877
55 XDI 0.8869
56 4JV 0.8865
57 VXP 0.8862
58 IM5 0.8856
59 M77 0.8855
60 QTV 0.8852
61 PU2 0.8848
62 6UW 0.8845
63 5V3 0.8841
64 C4F 0.8840
65 INI 0.8839
66 D4X 0.8836
67 SRE 0.8834
68 9E3 0.8831
69 LJ4 0.8830
70 G30 0.8826
71 TQ3 0.8825
72 SX3 0.8822
73 FNA 0.8820
74 CMP 0.8818
75 H35 0.8817
76 JE7 0.8815
77 5R9 0.8814
78 EXG 0.8805
79 BFS 0.8800
80 Q5M 0.8789
81 TQ4 0.8784
82 LFK 0.8778
83 DIH 0.8767
84 B4L 0.8754
85 HVE 0.8751
86 MQS 0.8747
87 VXM 0.8746
88 RB1 0.8746
89 GAT 0.8736
90 AOD 0.8736
91 FVV 0.8736
92 HO6 0.8732
93 FUZ 0.8727
94 ZEZ 0.8722
95 HN2 0.8720
96 CHJ 0.8715
97 7W7 0.8713
98 VGG 0.8707
99 5PK 0.8706
100 A7M 0.8689
101 F9W 0.8686
102 0OO 0.8682
103 B1T 0.8675
104 J90 0.8673
105 HN3 0.8658
106 7XX 0.8655
107 7KB 0.8654
108 4K2 0.8652
109 QRP 0.8647
110 T62 0.8646
111 GNG 0.8645
112 LLG 0.8644
113 LRT 0.8643
114 IMQ 0.8637
115 QNI 0.8633
116 CW6 0.8627
117 67B 0.8624
118 0QV 0.8614
119 00G 0.8614
120 GLA NPO 0.8603
121 PNJ 0.8603
122 RE4 0.8593
123 P2L 0.8592
124 WCU 0.8584
125 7PS 0.8578
126 MGI 0.8552
127 MG7 0.8546
128 YUG 0.8536
129 0NH 0.8522
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3QIN; Ligand: P1Y; 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: 3qin.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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