-->
Receptor
PDB id Resolution Class Description Source Keywords
1YOE 1.78 Å EC: 3.2.2.8 CRYSTAL STRUCTURE OF A THE E. COLI PYRIMIDINE NUCLEOSIDE HYD YBEK WITH BOUND RIBOSE ESCHERICHIA COLI PYRIMIDINE NUCLEOSIDE HYDROLASE BACTERIAL NUCLEOSIDASE RIBENZYME-PRODUCT COMPLEX HYDROLASE
Ref.: CRYSTAL STRUCTURE OF THE E. COLI PYRIMIDINE NUCLEOS HYDROLASE YBEK WITH BOUND RIBOSE TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1001;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
RIB A:2001;
Valid;
none;
submit data
150.13 C5 H10 O5 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1YOE 1.78 Å EC: 3.2.2.8 CRYSTAL STRUCTURE OF A THE E. COLI PYRIMIDINE NUCLEOSIDE HYD YBEK WITH BOUND RIBOSE ESCHERICHIA COLI PYRIMIDINE NUCLEOSIDE HYDROLASE BACTERIAL NUCLEOSIDASE RIBENZYME-PRODUCT COMPLEX HYDROLASE
Ref.: CRYSTAL STRUCTURE OF THE E. COLI PYRIMIDINE NUCLEOS HYDROLASE YBEK WITH BOUND RIBOSE TO BE PUBLISHED
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1YOE - RIB C5 H10 O5 C([C@@H]1[....
2 3G5I - DNB C11 H17 N3 O3 c1cc(c(cc1....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1YOE - RIB C5 H10 O5 C([C@@H]1[....
2 3G5I - DNB C11 H17 N3 O3 c1cc(c(cc1....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2MAS Kd = 30 nM PIR C11 H16 N2 O3 c1cc(ccc1[....
2 1YOE - RIB C5 H10 O5 C([C@@H]1[....
3 3G5I - DNB C11 H17 N3 O3 c1cc(c(cc1....
4 3MKN Ki = 76 uM DNB C11 H17 N3 O3 c1cc(c(cc1....
5 3B9X - NOS C10 H12 N4 O5 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RIB; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 AHR 1 1
2 FUB 1 1
3 32O 1 1
4 Z6J 1 1
5 RIB 1 1
6 GAL 0.653846 0.866667
7 GLC 0.653846 0.866667
8 BMA 0.653846 0.866667
9 WOO 0.653846 0.866667
10 GLA 0.653846 0.866667
11 BGC 0.653846 0.866667
12 MAN 0.653846 0.866667
13 GXL 0.653846 0.866667
14 ALL 0.653846 0.866667
15 GIV 0.653846 0.866667
16 FUB AHR 0.486486 0.875
17 AHR AHR 0.486486 0.875
18 G3F 0.483871 0.764706
19 2FG 0.483871 0.764706
20 1GN 0.483871 0.684211
21 GCS 0.483871 0.684211
22 SHG 0.483871 0.764706
23 2H5 0.483871 0.764706
24 PA1 0.483871 0.684211
25 GAF 0.483871 0.764706
26 X6X 0.483871 0.684211
27 95Z 0.483871 0.684211
28 G2F 0.483871 0.764706
29 3MG 0.46875 0.764706
30 SR1 0.466667 0.764706
31 2GS 0.454545 0.764706
32 FUB AHR AHR 0.45 0.875
33 AHR AHR AHR AHR AHR AHR 0.45 0.875
34 RP5 0.441176 0.675
35 HSX 0.441176 0.675
36 ABF 0.441176 0.675
37 GAL BGC 0.439024 0.742857
38 LBT 0.439024 0.742857
39 CBI 0.439024 0.742857
40 BMA GAL 0.439024 0.742857
41 B2G 0.439024 0.742857
42 GLA GLA 0.439024 0.742857
43 GLC GAL 0.439024 0.742857
44 N9S 0.439024 0.742857
45 BGC BMA 0.439024 0.742857
46 BGC GAL 0.439024 0.742857
47 MAL 0.439024 0.742857
48 MAB 0.439024 0.742857
49 GLA GAL 0.439024 0.742857
50 LAT 0.439024 0.742857
51 CBK 0.439024 0.742857
52 TRE 0.424242 0.742857
53 YIO 0.419355 0.757576
54 GLF 0.40625 0.735294
55 ALX 0.405405 0.619048
56 BNX 0.405405 0.619048
57 LB2 0.404762 0.742857
58 M3M 0.404762 0.742857
59 MAN GLC 0.404762 0.742857
60 NGR 0.404762 0.742857
61 GLA GAL BGC 0.4 0.742857
62 BGC BGC BGC BGC BGC BGC 0.4 0.742857
63 BGC BGC BGC BGC BGC 0.4 0.742857
64 BGC GLC GLC GLC 0.4 0.742857
65 CT3 0.4 0.742857
66 CEY 0.4 0.742857
67 GAL GAL GAL 0.4 0.742857
68 CE6 0.4 0.742857
69 B4G 0.4 0.742857
70 BMA MAN BMA 0.4 0.742857
71 GLC BGC BGC 0.4 0.742857
72 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.4 0.742857
73 MAN BMA BMA BMA BMA BMA 0.4 0.742857
74 GLA GAL GLC 0.4 0.742857
75 MT7 0.4 0.742857
76 GLC GLC BGC 0.4 0.742857
77 GLC GAL GAL 0.4 0.742857
78 CEX 0.4 0.742857
79 GLC GLC GLC GLC GLC 0.4 0.742857
80 DXI 0.4 0.742857
81 GLC BGC GLC 0.4 0.742857
82 CE5 0.4 0.742857
83 BGC BGC BGC BGC 0.4 0.742857
84 BGC GLC GLC GLC GLC GLC GLC 0.4 0.742857
85 CE8 0.4 0.742857
86 BGC GLC GLC GLC GLC 0.4 0.742857
87 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.4 0.742857
88 CTR 0.4 0.742857
89 BMA BMA BMA 0.4 0.742857
90 GLC BGC BGC BGC BGC BGC 0.4 0.742857
91 BMA BMA BMA BMA BMA 0.4 0.742857
92 CTT 0.4 0.742857
93 BMA BMA BMA BMA BMA BMA 0.4 0.742857
94 BGC GLC GLC 0.4 0.742857
95 MAN MAN BMA BMA BMA BMA 0.4 0.742857
96 GLC BGC BGC BGC BGC 0.4 0.742857
97 ASO 0.4 0.757576
98 BGC BGC GLC 0.4 0.742857
99 BGC BGC BGC 0.4 0.742857
100 MAN BMA BMA 0.4 0.742857
101 MLR 0.4 0.742857
102 BGC BGC BGC GLC 0.4 0.742857
103 MAN BMA BMA BMA BMA 0.4 0.742857
104 GLC BGC BGC BGC 0.4 0.742857
105 MTT 0.4 0.742857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: 38
This union binding pocket(no: 1) in the query (biounit: 1yoe.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5K4W THR 1.86916
2 4GNC ASO 2.00669
3 1I00 D16 2.06897
4 1I00 UMP 2.06897
5 1RX0 FAD 2.17391
6 1W8S FBP 2.6616
7 1ZCB GDP 2.79503
8 4BQ4 AAL GAL AAL GAL 2.79503
9 4ETZ C2E 3.367
10 2ODE ALF GDP 3.72671
11 1OJ7 NZQ 3.72671
12 4D9C PMP 4.34783
13 1J0D 5PA 4.65839
14 3CLH NAD 4.65839
15 3ZOK NAD 5.2795
16 1S16 ANP 5.2795
17 1FQJ GDP 5.44218
18 1FQK GDP 5.44218
19 3AB3 GDP 6.09756
20 3QT6 2P0 6.52174
21 4DVE BTN 7.07071
22 1SVK ALF GDP 7.45342
23 1Y3A GDP 7.45342
24 6CRK GDP 7.45342
25 2OM2 GDP 7.45342
26 4P6C RES 7.56302
27 1BH2 GSP 7.61905
28 1QZR ANP 7.76398
29 4H53 SLB 8.69565
30 6AU6 GDP 12.1118
31 1CS4 GSP 12.1118
32 5KDO GDP 13.5135
33 1GOT GDP 13.6986
34 2NNQ T4B 13.7405
35 1ZXM ANP 14.5963
36 4P5F AR6 21.118
37 4I71 AGV 33.5404
38 3EPW JMQ 38.1988
Pocket No.: 2; Query (leader) PDB : 1YOE; Ligand: RIB; 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: 1yoe.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1yoe.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1yoe.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1yoe.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1yoe.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 1yoe.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1yoe.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 1yoe.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 1yoe.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 1yoe.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 1YOE; Ligand: RIB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 1yoe.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback