Receptor
PDB id Resolution Class Description Source Keywords
4YJK 1.68 Å EC: 2.4.2.3 CRYSTAL STRUCTURE OF C212S MUTANT OF SHEWANELLA ONEIDENSIS M URIDINE PHOSPHORYLASE SHEWANELLA ONEIDENSIS (STRAIN MR-1) URACIL S212C MUTANT URIDINE PHOSPHORYLASE TRANSFERASE
Ref.: CONCERTED ACTION OF TWO SUBUNITS OF THE FUNCTIONAL SHEWANELLA ONEIDENSIS MR-1 URIDINE PHOSPHORYLASE DE FROM A COMPARISON OF THE C212S MUTANT AND THE WILD-ENZYME. ACTA CRYSTALLOGR D STRUCT V. 72 203 2016 BIOL
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:301;
E:301;
F:302;
A:302;
C:301;
D:302;
D:304;
E:302;
D:303;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
URA F:301;
D:301;
A:301;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
112.087 C4 H4 N2 O2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YJK 1.68 Å EC: 2.4.2.3 CRYSTAL STRUCTURE OF C212S MUTANT OF SHEWANELLA ONEIDENSIS M URIDINE PHOSPHORYLASE SHEWANELLA ONEIDENSIS (STRAIN MR-1) URACIL S212C MUTANT URIDINE PHOSPHORYLASE TRANSFERASE
Ref.: CONCERTED ACTION OF TWO SUBUNITS OF THE FUNCTIONAL SHEWANELLA ONEIDENSIS MR-1 URIDINE PHOSPHORYLASE DE FROM A COMPARISON OF THE C212S MUTANT AND THE WILD-ENZYME. ACTA CRYSTALLOGR D STRUCT V. 72 203 2016 BIOL
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4YJK - URA C4 H4 N2 O2 C1=CNC(=O)....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1U1G - BBB C21 H22 N2 O6 c1ccc(cc1)....
2 1RXC - R1P C5 H11 O8 P C([C@@H]1[....
3 1TGY - R1P C5 H11 O8 P C([C@@H]1[....
4 4E1V - URF C4 H3 F N2 O2 C1=C(C(=O)....
5 1U1E - 182 C13 H14 N2 O4 Se c1ccc(cc1)....
6 3KVV - URF C4 H3 F N2 O2 C1=C(C(=O)....
7 1U1D - 181 C13 H14 N2 O4 S c1ccc(cc1)....
8 1U1C Ki ~ 4300 nM BAU C14 H16 N2 O4 c1ccc(cc1)....
9 3FWP - ANU C9 H10 N2 O5 C1=CN2[C@H....
10 1TGV - 5UD C9 H11 F N2 O6 C1=C(C(=O)....
11 1U1F Ki ~ 680 nM 183 C21 H22 N2 O5 c1ccc(cc1)....
12 4YJK - URA C4 H4 N2 O2 C1=CNC(=O)....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1U1G - BBB C21 H22 N2 O6 c1ccc(cc1)....
2 1RXC - R1P C5 H11 O8 P C([C@@H]1[....
3 1TGY - R1P C5 H11 O8 P C([C@@H]1[....
4 4E1V - URF C4 H3 F N2 O2 C1=C(C(=O)....
5 1U1E - 182 C13 H14 N2 O4 Se c1ccc(cc1)....
6 3KVV - URF C4 H3 F N2 O2 C1=C(C(=O)....
7 1U1D - 181 C13 H14 N2 O4 S c1ccc(cc1)....
8 1U1C Ki ~ 4300 nM BAU C14 H16 N2 O4 c1ccc(cc1)....
9 3FWP - ANU C9 H10 N2 O5 C1=CN2[C@H....
10 1TGV - 5UD C9 H11 F N2 O6 C1=C(C(=O)....
11 1U1F Ki ~ 680 nM 183 C21 H22 N2 O5 c1ccc(cc1)....
12 4YJK - URA C4 H4 N2 O2 C1=CNC(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: URA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 URA 1 1
2 TUL 0.5 0.725
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YJK; Ligand: URA; Similar sites found: 106
This union binding pocket(no: 1) in the query (biounit: 4yjk.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5AHW CMP 0.01066 0.41218 None
2 5J8O 6GZ 0.01332 0.40817 None
3 5DX0 SFG 0.03965 0.40161 0.793651
4 4J3L AJ5 0.02536 0.40241 1.42857
5 5J75 6GQ 0.01168 0.40448 1.51515
6 5U3F 7TS 0.007236 0.43083 1.98413
7 5LX6 78P 0.01564 0.40151 2.09424
8 3DUW SAH 0.0008643 0.48621 2.24215
9 3LGS ADE 0.00001577 0.41902 2.38095
10 3LGS SAH 0.00001577 0.41902 2.38095
11 1I9G SAM 0.01303 0.41461 2.38095
12 5KJZ PCG 0.00951 0.41882 2.66667
13 1NFS DED 0.01676 0.40761 2.73224
14 2XIQ MLC 0.008424 0.44009 2.77778
15 2PCU PHE ASN ARG PRO VAL 0.00382 0.42505 2.77778
16 3X0D SAH 0.01008 0.42442 2.77778
17 4ZH7 FUC GAL NAG GAL FUC 0.008778 0.41381 2.77778
18 4Z9D NAD 0.01408 0.4168 2.85714
19 4QAR ADE 0.000006665 0.45763 2.98507
20 5EWK P34 0.0004193 0.44517 3
21 1PJS SAH 0.003634 0.4425 3.1746
22 5KJW 53C 0.003117 0.41258 3.1746
23 4AZW SAM 0.02119 0.4075 3.1746
24 2Y6Q I7T 0.0473 0.40676 3.1746
25 3IES M24 0.04193 0.4031 3.1746
26 5N5D SAM 0.001066 0.48227 3.53982
27 5IFK HPA 0.0001424 0.47557 3.57143
28 1GAD NAD 0.02831 0.43333 3.57143
29 1Q19 APC 0.006496 0.43098 3.57143
30 4GV4 MEJ 0.01784 0.41185 3.57143
31 5F7J ADE 0.00001103 0.41161 3.57143
32 4I8P NAD 0.02383 0.41127 3.57143
33 4KIB SAH 0.01837 0.41039 3.57143
34 2E7Z MGD 0.03863 0.40725 3.57143
35 3H8V ATP 0.03097 0.40071 3.57143
36 5OFW 9TW 0.004283 0.40995 3.58744
37 5DYO FLU 0.004874 0.41117 3.66972
38 4FK7 P34 0.0005662 0.45237 3.93013
39 1C3X 8IG 0.0007972 0.44834 3.96825
40 4DE9 VTP 0.007184 0.43673 3.96825
41 4K91 SIN 0.005257 0.41216 3.96825
42 2E0N SAH 0.01152 0.41183 3.96825
43 4GYW UDP 0.04528 0.40632 3.96825
44 2ZMF CMP 0.001377 0.46438 4.2328
45 2P4S DIH 0.0001056 0.51268 4.36508
46 4CE5 PDG 0.004613 0.44764 4.36508
47 4UUG PXG 0.004818 0.44446 4.36508
48 2IHT TPP 0.01802 0.41298 4.36508
49 4L2I NAD 0.04693 0.41246 4.36508
50 1G2O IMH 0.0001745 0.40805 4.36508
51 3VPH NAD 0.03236 0.40784 4.36508
52 1TMM APC 0.03273 0.40789 4.43038
53 3SM2 478 0.02702 0.42235 4.54545
54 4R0M FA5 0.03737 0.40285 4.7619
55 5M3E APR 0.0421 0.4004 4.84848
56 1VMK GUN 0.0001733 0.49166 5.05415
57 5N53 8NB 0.003123 0.40767 5.12821
58 4C4A SAH 0.01299 0.41878 5.15873
59 3IWJ NAD 0.01598 0.4002 5.15873
60 2RDE C2E 0.0009738 0.46233 5.57769
61 5UAV NDP 0.04683 0.40705 5.95238
62 3BOF HCS 0.01254 0.40359 5.95238
63 2OQ2 A3P 0.02325 0.41029 6.34921
64 5KVA SAM 0.008872 0.42635 6.47482
65 5UKL SIX 0.00846 0.43119 6.48968
66 3FHI ANP 0.02151 0.40772 7.14286
67 1MJH ATP 0.01588 0.40883 7.40741
68 1OG1 TAD 0.01926 0.40823 7.52212
69 1Q0S SAH 0.02925 0.40433 7.53968
70 5ETJ IM5 0.0003305 0.52794 7.93651
71 2QQF A1R 0.01666 0.42458 7.93651
72 3OV6 MK0 0.01856 0.42051 7.93651
73 1E6E FAD 0.03896 0.41389 7.93651
74 1D4D FAD 0.0388 0.41236 7.93651
75 3NRR D16 0.03685 0.41671 8.33333
76 5LOG SAH 0.002129 0.46081 8.58369
77 4XUC SAM 0.01842 0.431 8.7156
78 4XUC 43G 0.01842 0.431 8.7156
79 4DR9 BB2 0.01713 0.40268 8.85417
80 2A92 NAI 0.009234 0.44446 9.12698
81 3AWJ COA 0.0201 0.40443 9.12698
82 3QOX SAH 0.03637 0.4013 9.12698
83 3L9R L9R 0.04719 0.40374 9.18367
84 4MIG G3F 0.0173 0.43928 9.52381
85 3JSX CC2 0.04355 0.43431 9.52381
86 3JSX FAD 0.01219 0.43065 9.52381
87 1Q3Q ANP 0.03056 0.40658 9.52381
88 3KJS NAP 0.02284 0.41799 10.3175
89 3KJS DQ1 0.0356 0.41799 10.3175
90 2A8Y MTA 0.0001333 0.52441 11.9048
91 1T90 NAD 0.03383 0.40348 11.9048
92 1VKF CIT 0.004058 0.42386 12.234
93 4WKB TDI 0.00002429 0.56747 12.2951
94 3DJF BC3 0.000194 0.51827 12.6984
95 2XZ9 PYR 0.004555 0.42015 17.8571
96 4BMX ADE 0.00002099 0.56747 27.0916
97 3KVY URA 0.00000000005933 0.82875 33.3333
98 3KVY R2B 0.0008615 0.46833 33.3333
99 1ZOS MTM 0.00001607 0.4367 33.913
100 1NW4 IMH 0.00001934 0.4421 37.3016
101 1ODJ GMP 0.0000005493 0.48689 40.8511
102 3BJE URA 0.0000000000915 0.81639 40.873
103 1VHW ADN 0.000002915 0.48955 40.873
104 3U40 ADN 0.0000007282 0.6382 43.3884
105 5MX4 HPA 0.0000004161 0.59771 43.7768
106 1A69 FMB 0.01725 0.47635 44.5378
Pocket No.: 2; Query (leader) PDB : 4YJK; Ligand: URA; 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: 4yjk.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4YJK; Ligand: URA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4yjk.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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