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 1256 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: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 UMP 1 1
2 DU 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 DUT MG 0.684932 0.914286
10 DUR 0.683333 0.852941
11 UMP AF3 PO4 0.675676 0.876712
12 DDN 0.632353 1
13 UFP 0.591549 0.929577
14 BRU 0.583333 0.929577
15 5HU 0.583333 0.942857
16 TMP 0.583333 0.956522
17 UM3 0.57971 0.955224
18 5IU 0.575342 0.929577
19 DCM 0.561644 0.928571
20 DC 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U5P 0.527778 0.911765
24 DDU 0.523077 0.753623
25 UMC 0.520548 0.941176
26 QBT 0.493333 0.927536
27 DUA 0.487805 0.783784
28 DU3 0.487805 0.780822
29 DU4 0.47619 0.76
30 TYD 0.469136 0.942857
31 YYY 0.451219 0.915493
32 UDP 0.45 0.898551
33 TTP 0.447059 0.942857
34 8OG 0.435294 0.835443
35 UA3 0.434211 0.897059
36 U3P 0.434211 0.897059
37 U2P 0.434211 0.884058
38 UTP 0.433735 0.898551
39 44P 0.43038 0.914286
40 DCP 0.430233 0.915493
41 DUX 0.411765 0.756757
42 2KH 0.411765 0.873239
43 UMF 0.410256 0.84507
44 139 0.409091 0.8
45 UPU 0.409091 0.871429
46 U 0.408451 0.771429
47 URI 0.408451 0.771429
48 TBD 0.406977 0.90411
49 PUA 0.405172 0.833333
50 UNP 0.402299 0.873239
51 UDX 0.4 0.873239
52 UAD 0.4 0.873239
53 PUP 0.4 0.955882
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5HX1; Ligand: UMP; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 5hx1.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5BVS EIC 0.01272 0.41207 None
2 4D9C PMP 0.01777 0.41874 4.34783
3 4E1O PLP PVH 0.02946 0.40125 4.34783
4 2B4G FMN 0.04065 0.40063 4.34783
5 1VLH PNS 0.0201 0.40731 5.07246
6 4ZLU ADP 0.04216 0.40808 5.7971
7 4ZLU 4PW 0.04216 0.40808 5.7971
8 1J0D 5PA 0.02764 0.40768 5.7971
9 2PK3 GDD 0.03424 0.40481 5.7971
10 4USF 6UI 0.03188 0.40323 5.7971
11 1DNP FAD 0.04314 0.40067 5.7971
12 5MIL DUP 0.0004831 0.48873 7.24638
13 2Z3U CRR 0.005554 0.45108 7.97101
14 5FVJ ACO 0.03891 0.40203 7.97101
15 1ZDT PEF 0.04066 0.40137 9.42029
16 2QCD U5P 0.01653 0.41284 10.8696
17 3G4G D71 0.01926 0.40751 10.8696
18 4HKP TKW 0.02536 0.40677 10.8696
19 5U98 1KX 0.02956 0.43416 13.1313
20 1EU1 MGD 0.01651 0.43422 19.5652
21 1W2Y DUN 0.0004526 0.49547 20.2899
22 5HZ9 5M8 0.01136 0.41809 24.6377
Pocket No.: 2; Query (leader) PDB : 5HX1; Ligand: UMP; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 5hx1.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1G2N EPH 0.03596 0.40021 2.89855
2 1B8O IMH 0.03502 0.40264 7.24638
3 1YMT DR9 0.04246 0.40151 9.42029
4 2AEL SAZ 0.02425 0.40335 10.1449
5 4WZA ACP 0.04574 0.42247 10.8696
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