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: 83
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 6OG 0.465909 0.884615
19 A3P 0.465116 0.855263
20 ABM 0.458824 0.810127
21 AMP 0.457831 0.855263
22 A 0.457831 0.855263
23 HF7 0.457447 0.907895
24 3AD 0.454545 0.75
25 SAP 0.450549 0.884615
26 AGS 0.450549 0.884615
27 A2P 0.448276 0.866667
28 MDR 0.443038 0.74026
29 A2D 0.44186 0.810127
30 3AT 0.44086 0.857143
31 7D3 0.436782 0.822785
32 PPS 0.43617 0.819277
33 PAP 0.434783 0.844156
34 2AM 0.433735 0.855263
35 ADX 0.433333 0.797619
36 BA3 0.431818 0.810127
37 AP2 0.431818 0.848101
38 A12 0.431818 0.848101
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 ADS THS THS THS 0.423729 0.813953
46 AT4 0.422222 0.871795
47 AN2 0.422222 0.822785
48 7D7 0.421053 0.714286
49 ATR 0.419355 0.855263
50 OVE 0.418605 0.894737
51 CA0 0.417582 0.790123
52 AU1 0.417582 0.8125
53 7D4 0.417582 0.822785
54 M33 0.417582 0.8
55 RAB 0.415584 0.717949
56 ADN 0.415584 0.717949
57 XYA 0.415584 0.717949
58 CL9 0.414634 0.7625
59 ATP 0.413043 0.833333
60 ACP 0.413043 0.835443
61 50T 0.413043 0.822785
62 HEJ 0.413043 0.833333
63 A1R 0.41 0.85
64 AQP 0.408602 0.833333
65 APC 0.408602 0.848101
66 2A5 0.408602 0.858974
67 AR6 0.408602 0.810127
68 5FA 0.408602 0.833333
69 APR 0.408602 0.810127
70 DG DA DC DG 0.407407 0.781609
71 DG 0.406593 0.85
72 DGP 0.406593 0.85
73 5N5 0.405063 0.696203
74 ADV 0.404255 0.825
75 RBY 0.404255 0.825
76 AD9 0.404255 0.8125
77 DA DC DG DA 0.402878 0.811765
78 CC5 0.402597 0.736842
79 NA7 0.401961 0.871795
80 A A A 0.401961 0.846154
81 5CD 0.4 0.705128
82 3DH 0.4 0.7
83 A4D 0.4 0.717949
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FBF; Ligand: DCM; 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: 5fbf.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5FBF; Ligand: DCM; 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: 5fbf.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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