Receptor
PDB id Resolution Class Description Source Keywords
5FBC 1.75 Å EC: 3.1.30.1 S1 NUCLEASE FROM ASPERGILLUS ORYZAE IN COMPLEX WITH 2'-DEOXY 5'-THIO-MONOPHOSPHATE (5'DAMP(S)). ASPERGILLUS ORYZAE RIB40 ENDONUCLEASE ZINC DEPENDENT COMPLEX HYDROLASE
Ref.: STRUCTURAL AND CATALYTIC PROPERTIES OF S1 NUCLEASE ASPERGILLUS ORYZAE RESPONSIBLE FOR SUBSTRATE RECOGN CLEAVAGE, NON-SPECIFICITY, AND INHIBITION. PLOS ONE V. 11 68832 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AS A:601;
Valid;
none;
submit data
347.287 C10 H14 N5 O5 P S c1nc(...
ZN A:402;
A:401;
A:403;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
NAG A:501;
A:502;
Invalid;
Invalid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
GOL A:701;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FBF 1.04 Å EC: 3.1.30.1 S1 NUCLEASE FROM ASPERGILLUS ORYZAE IN COMPLEX WITH TWO MOLE 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE ASPERGILLUS ORYZAE RIB40 ENDONUCLEASE ZINC DEPENDENT COMPLEX HYDROLASE
Ref.: STRUCTURAL AND CATALYTIC PROPERTIES OF S1 NUCLEASE ASPERGILLUS ORYZAE RESPONSIBLE FOR SUBSTRATE RECOGN CLEAVAGE, NON-SPECIFICITY, AND INHIBITION. PLOS ONE V. 11 68832 2016
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5FBB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5FBC - AS C10 H14 N5 O5 P S c1nc(c2c(n....
3 5FBF - DCM C9 H14 N3 O7 P C1[C@@H]([....
4 5FBD - DCZ C9 H13 N3 O4 C1[C@@H]([....
5 5FBG - GNG C10 H13 N5 O4 c1nc2c(n1[....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5FBB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5FBC - AS C10 H14 N5 O5 P S c1nc(c2c(n....
3 5FBF - DCM C9 H14 N3 O7 P C1[C@@H]([....
4 5FBD - DCZ C9 H13 N3 O4 C1[C@@H]([....
5 5FBG - GNG C10 H13 N5 O4 c1nc2c(n1[....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5FBB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5FBC - AS C10 H14 N5 O5 P S c1nc(c2c(n....
3 5FBF - DCM C9 H14 N3 O7 P C1[C@@H]([....
4 5FBD - DCZ C9 H13 N3 O4 C1[C@@H]([....
5 5FBG - GNG C10 H13 N5 O4 c1nc2c(n1[....
6 1AK0 - ADS THS THS THS n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AS; Similar ligands found: 81
No: Ligand ECFP6 Tc MDL keys Tc
1 AS 1 1
2 D5M 0.808824 0.945205
3 DA 0.808824 0.945205
4 DAT 0.733333 0.92
5 DTP 0.696203 0.92
6 3L1 0.671642 0.789474
7 3D1 0.671642 0.789474
8 5F1 0.652174 0.773333
9 SRA 0.564103 0.907895
10 101 0.564103 0.893333
11 CPA 0.54902 0.819277
12 DOI 0.548781 0.868421
13 103 0.531646 0.805195
14 7D5 0.475 0.844156
15 DA DT DA DA 0.474576 0.788235
16 DDS 0.472527 0.868421
17 ZDA 0.466667 0.78481
18 A3P 0.465116 0.855263
19 ABM 0.458824 0.810127
20 AMP 0.457831 0.855263
21 A 0.457831 0.855263
22 3AD 0.454545 0.75
23 DU DU DU DU BRU DA DU 0.451613 0.770115
24 AGS 0.450549 0.884615
25 SAP 0.450549 0.884615
26 A2P 0.448276 0.866667
27 MDR 0.443038 0.74026
28 A2D 0.44186 0.810127
29 3AT 0.44086 0.857143
30 7D3 0.436782 0.822785
31 PPS 0.43617 0.819277
32 PAP 0.434783 0.844156
33 2AM 0.433735 0.855263
34 ADX 0.433333 0.797619
35 BA3 0.431818 0.810127
36 A12 0.431818 0.848101
37 AP2 0.431818 0.848101
38 AMP MG 0.430233 0.7875
39 3AM 0.428571 0.842105
40 AP5 0.426966 0.810127
41 ADP 0.426966 0.833333
42 B4P 0.426966 0.810127
43 2FD 0.426829 0.7625
44 PRX 0.423913 0.8125
45 AN2 0.422222 0.822785
46 7D7 0.421053 0.714286
47 ATR 0.419355 0.855263
48 OVE 0.418605 0.894737
49 CA0 0.417582 0.790123
50 M33 0.417582 0.8
51 7D4 0.417582 0.822785
52 AU1 0.417582 0.8125
53 RAB 0.415584 0.717949
54 ADN 0.415584 0.717949
55 XYA 0.415584 0.717949
56 DA DC DG DA 0.414815 0.781609
57 CL9 0.414634 0.7625
58 ACP 0.413043 0.835443
59 50T 0.413043 0.822785
60 ATP 0.413043 0.833333
61 A1R 0.41 0.85
62 2A5 0.408602 0.858974
63 AR6 0.408602 0.810127
64 APC 0.408602 0.848101
65 5FA 0.408602 0.833333
66 APR 0.408602 0.810127
67 AQP 0.408602 0.833333
68 DG DA DC DG 0.407407 0.781609
69 DG 0.406593 0.85
70 DGP 0.406593 0.85
71 5N5 0.405063 0.696203
72 ADV 0.404255 0.825
73 RBY 0.404255 0.825
74 AD9 0.404255 0.8125
75 CC5 0.402597 0.736842
76 ADP MG 0.402174 0.777778
77 NA7 0.401961 0.871795
78 A A A 0.401961 0.846154
79 A4D 0.4 0.717949
80 3DH 0.4 0.7
81 5CD 0.4 0.705128
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FBF; Ligand: DCM; Similar sites found: 3
This union binding pocket(no: 1) in the query (biounit: 5fbf.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Y79 GLY ASP 0.008107 0.40173 3.37079
2 1M5W DXP 0.02266 0.40611 6.17284
3 1P6D 3PC 0.000001663 0.56129 14.2857
Pocket No.: 2; Query (leader) PDB : 5FBF; Ligand: DCM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5fbf.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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