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Receptor
PDB id Resolution Class Description Source Keywords
5HX1 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF DR2231_E46A MUTANT IN COMPLEX WITH DUMP MAGNESIUM DEINOCOCCUS RADIODURANS ALPHA HELIX METAL BINDING PROTEIN
Ref.: DEINOCOCCUS RADIODURANS DR2231 IS A TWO-METAL-ION M HYDROLASE WITH EXCLUSIVE ACTIVITY ON DUTP. FEBS J. V. 283 4274 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG D:201;
B:202;
A:202;
C:201;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
UMP B:201;
A:201;
Valid;
Valid;
none;
none;
submit data
308.182 C9 H13 N2 O8 P C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5HX1 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF DR2231_E46A MUTANT IN COMPLEX WITH DUMP MAGNESIUM DEINOCOCCUS RADIODURANS ALPHA HELIX METAL BINDING PROTEIN
Ref.: DEINOCOCCUS RADIODURANS DR2231 IS A TWO-METAL-ION M HYDROLASE WITH EXCLUSIVE ACTIVITY ON DUTP. FEBS J. V. 283 4274 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5HX1 - UMP C9 H13 N2 O8 P C1[C@@H]([....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2YFD - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 5HZZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5HYL - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 5HWU Kd = 5.35 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 5I0M - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 2YFC - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 5HVA Kd = 0.086 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 5I0J - UMP C9 H13 N2 O8 P C1[C@@H]([....
9 5HX1 - UMP C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2YFD - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 5HZZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5HYL - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 5HWU Kd = 5.35 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 5I0M - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 2YFC - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 5HVA Kd = 0.086 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 5I0J - UMP C9 H13 N2 O8 P C1[C@@H]([....
9 5HX1 - UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UMP; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 DU 1 1
2 UMP 1 1
3 DUD 0.8 0.985075
4 UC5 0.772727 0.970588
5 DUT 0.753623 0.985075
6 DUN 0.75 0.956522
7 DUP 0.742857 0.956522
8 DUS 0.692308 0.853333
9 DUR 0.683333 0.852941
10 DDN 0.632353 1
11 UFP 0.591549 0.929577
12 TMP 0.583333 0.956522
13 BRU 0.583333 0.929577
14 5HU 0.583333 0.942857
15 UM3 0.57971 0.955224
16 5IU 0.575342 0.929577
17 DC 0.561644 0.928571
18 DCM 0.561644 0.928571
19 BVP 0.531646 0.942857
20 DU DU DU DU BRU DU DU 0.53125 0.864865
21 U 0.527778 0.911765
22 U5P 0.527778 0.911765
23 DDU 0.523077 0.753623
24 UMC 0.520548 0.941176
25 QBT 0.493333 0.927536
26 DUA 0.487805 0.783784
27 DU3 0.487805 0.780822
28 DU4 0.47619 0.76
29 TYD 0.469136 0.942857
30 YYY 0.451219 0.915493
31 UDP 0.45 0.898551
32 TTP 0.447059 0.942857
33 8OG 0.435294 0.835443
34 U3P 0.434211 0.897059
35 UA3 0.434211 0.897059
36 U2P 0.434211 0.884058
37 UTP 0.433735 0.898551
38 44P 0.43038 0.914286
39 DCP 0.430233 0.915493
40 2KH 0.411765 0.873239
41 DUX 0.411765 0.756757
42 UMF 0.410256 0.84507
43 139 0.409091 0.8
44 UPU 0.409091 0.871429
45 URI 0.408451 0.771429
46 TBD 0.406977 0.90411
47 DU DU DU DU BRU DA DU 0.40625 0.771084
48 PUA 0.405172 0.833333
49 UNP 0.402299 0.873239
50 UDX 0.4 0.873239
51 PUP 0.4 0.955882
52 UAD 0.4 0.873239
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5HX1; Ligand: UMP; Similar sites found with APoc: 36
This union binding pocket(no: 1) in the query (biounit: 5hx1.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1PU7 39A None
2 2WAT COA None
3 5BVS EIC None
4 5JBE GLC GLC GLC GLC GLC 2.89855
5 5IVE 6E8 3.33333
6 1H3F TYE 3.62319
7 4D9C PMP 4.34783
8 4E1O PLP PVH 4.34783
9 2GMH FAD 5.07246
10 1VLH PNS 5.07246
11 2IHK CSF 5.7971
12 4ZLU 4PW 5.7971
13 4ZLU ADP 5.7971
14 1J0D 5PA 5.7971
15 2PK3 GDD 5.7971
16 4USF 6UI 5.7971
17 1DNP FAD 5.7971
18 1EP2 FMN 6.52174
19 5MIL DUP 7.24638
20 2YAY DUP 7.24638
21 2Z3U CRR 7.97101
22 5FVJ ACO 7.97101
23 5MYD DUP 8.69565
24 1ZDT PEF 9.42029
25 6H3O FAD 10.8696
26 2QCD U5P 10.8696
27 3G4G D71 10.8696
28 4HKP TKW 10.8696
29 4DL8 UMP AF3 PO4 13.0435
30 6FCX SAH 15.942
31 5WX3 COA 17.3913
32 1EU1 MGD 19.5652
33 1W2Y DUN 20.2899
34 5W8Q BU4 23.1884
35 5HZ9 5M8 24.6377
36 3WBG 2AN 24.6377
Pocket No.: 2; Query (leader) PDB : 5HX1; Ligand: UMP; Similar sites found with APoc: 11
This union binding pocket(no: 2) in the query (biounit: 5hx1.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1G2N EPH 2.89855
2 1B8O IMH 7.24638
3 6ALW BNV 7.97101
4 6ALW BMJ 7.97101
5 1YMT DR9 9.42029
6 2AEL SAZ 10.1449
7 4WZA ADP 10.8696
8 4WZA ACP 10.8696
9 4P5E N6P 19.5652
10 5Y02 HBX 21.0145
11 6EPY RAF 27.5362
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