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 (2D)
Ligand no: 1; Ligand: AS; Similar ligands found: 88
No: Ligand ECFP6 Tc MDL keys Tc
1 AS 1 1
2 DA 0.808824 0.945205
3 D5M 0.808824 0.945205
4 DAT 0.733333 0.92
5 DTP 0.696203 0.92
6 DZ4 0.6875 0.896104
7 3D1 0.671642 0.789474
8 3L1 0.671642 0.789474
9 5F1 0.652174 0.773333
10 101 0.564103 0.893333
11 SRA 0.564103 0.907895
12 CPA 0.54902 0.819277
13 6MA 0.548781 0.906667
14 DOI 0.548781 0.868421
15 103 0.531646 0.805195
16 7D5 0.475 0.844156
17 KF5 0.472973 0.618421
18 DDS 0.472527 0.868421
19 ZDA 0.466667 0.78481
20 6OG 0.465909 0.884615
21 A3P 0.465116 0.855263
22 CUU 0.460674 0.857143
23 45A 0.458824 0.810127
24 ABM 0.458824 0.810127
25 AMP 0.457831 0.855263
26 A 0.457831 0.855263
27 HF7 0.457447 0.907895
28 3AD 0.454545 0.75
29 AGS 0.450549 0.884615
30 A2P 0.448276 0.866667
31 MDR 0.443038 0.74026
32 A2D 0.44186 0.810127
33 3AT 0.44086 0.857143
34 7D3 0.436782 0.822785
35 PPS 0.43617 0.819277
36 AMP MG 0.435294 0.818182
37 PAP 0.434783 0.844156
38 2AM 0.433735 0.855263
39 ADX 0.433333 0.797619
40 AP2 0.431818 0.848101
41 BA3 0.431818 0.810127
42 A12 0.431818 0.848101
43 3AM 0.428571 0.842105
44 ADP 0.426966 0.833333
45 B4P 0.426966 0.810127
46 AP5 0.426966 0.810127
47 2FD 0.426829 0.7625
48 PRX 0.423913 0.8125
49 ADS THS THS THS 0.423729 0.813953
50 AT4 0.422222 0.871795
51 AN2 0.422222 0.822785
52 7D7 0.421053 0.714286
53 ATR 0.419355 0.855263
54 OVE 0.418605 0.894737
55 M33 0.417582 0.8
56 7D4 0.417582 0.822785
57 CA0 0.417582 0.790123
58 AU1 0.417582 0.8125
59 XYA 0.415584 0.717949
60 ADN 0.415584 0.717949
61 RAB 0.415584 0.717949
62 CL9 0.414634 0.7625
63 50T 0.413043 0.822785
64 HEJ 0.413043 0.833333
65 ACP 0.413043 0.835443
66 ATP 0.413043 0.833333
67 KG4 0.413043 0.790123
68 A1R 0.41 0.85
69 APC 0.408602 0.848101
70 AR6 0.408602 0.810127
71 APR 0.408602 0.810127
72 2A5 0.408602 0.858974
73 5FA 0.408602 0.833333
74 AQP 0.408602 0.833333
75 HQG 0.408163 0.822785
76 ADP BEF 0.406593 0.807692
77 ADP MG 0.406593 0.807692
78 DGP 0.406593 0.85
79 DG 0.406593 0.85
80 5N5 0.405063 0.696203
81 RBY 0.404255 0.825
82 ADV 0.404255 0.825
83 AD9 0.404255 0.8125
84 CC5 0.402597 0.736842
85 NA7 0.401961 0.871795
86 A4D 0.4 0.717949
87 5CD 0.4 0.705128
88 3DH 0.4 0.7
Similar Ligands (3D)
Ligand no: 1; Ligand: AS; Similar ligands found: 83
No: Ligand Similarity coefficient
1 TMP 0.9562
2 UMP 0.9552
3 IMP 0.9530
4 G 0.9519
5 5GP 0.9446
6 FMP 0.9418
7 DI 0.9408
8 IRP 0.9392
9 5CM 0.9383
10 NYM 0.9323
11 5HU 0.9305
12 AMZ 0.9302
13 C 0.9289
14 U5P 0.9273
15 5IU 0.9246
16 IMU 0.9237
17 BMP 0.9235
18 C2R 0.9224
19 MTA 0.9216
20 FDM 0.9214
21 8OP 0.9210
22 UP6 0.9192
23 Z8B 0.9187
24 8OG 0.9186
25 C5P 0.9177
26 QBT 0.9175
27 DC 0.9169
28 5FU 0.9167
29 XMP 0.9155
30 BMQ 0.9154
31 DCM 0.9151
32 ZAS 0.9141
33 NEC 0.9116
34 8GM 0.9113
35 U 0.9107
36 BVP 0.9101
37 NUP 0.9096
38 T3S 0.9093
39 N5O 0.9091
40 PFU 0.9088
41 6MZ 0.9083
42 DU 0.9077
43 5BU 0.9074
44 G7M 0.9058
45 AOC 0.9053
46 CNU 0.9048
47 NIA 0.9046
48 FNU 0.9043
49 TKW 0.9040
50 9L3 0.9036
51 NMN 0.9036
52 6RE 0.9028
53 CAR 0.9016
54 J7C 0.9016
55 A3N 0.9012
56 DDN 0.8990
57 D4M 0.8967
58 2DT 0.8967
59 71V 0.8954
60 UFP 0.8944
61 S5P 0.8936
62 UMC 0.8935
63 DOC 0.8914
64 JLN 0.8900
65 ATM 0.8898
66 16B 0.8881
67 NCN 0.8877
68 4X2 0.8870
69 93A 0.8849
70 DUS 0.8848
71 2GE 0.8840
72 GJV 0.8826
73 U6M 0.8822
74 NWQ 0.8812
75 BRU 0.8811
76 460 0.8794
77 PSU 0.8706
78 GDP 0.8705
79 MCF 0.8671
80 6CG 0.8637
81 C2P 0.8637
82 IDP 0.8591
83 IMH 0.8576
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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