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Receptor
PDB id Resolution Class Description Source Keywords
1Z4I 1.98 Å EC: 3.1.3.5 STRUCTURE OF THE D41N VARIANT OF THE HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH DEOXYRIBOURIDINE 5'- M ONOPHOSPHATE HOMO SAPIENS ALFA BETA FOLD HYDROLASE
Ref.: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY OF THE H MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE STRUCTURE V. 13 1081 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:2001;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:1228;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
UMP A:1001;
Valid;
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
4L6C 1.8 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDA COMPLEX WITH THE INHIBITOR PIB-T HOMO SAPIENS 5-prime -NUCLEOTIDASE MITOCHONDRIA PROTEIN CONFORMATION SEQUENCHOMOLOGY HAD-LIKE HYDROLASE DEPHOSPHORYLATION PHOSPHORYHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: CONFORMATIONALLY CONSTRAINED NUCLEOSIDE PHOSPHONIC POTENT INHIBITORS OF HUMAN MITOCHONDRIAL AND CYTOSO 5'(3')-NUCLEOTIDASES. ORG.BIOMOL.CHEM. V. 12 7971 2014
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1Q92 - DRM C10 H15 N2 O6 P C1C[C@H]([....
2 1Z4P - DGP C10 H14 N5 O7 P c1nc2c(n1[....
3 1Z4M - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4NFL Ki = 22.1 uM 2JW C17 H18 N3 O10 P CC1=CN(C(=....
5 1Q91 Ki = 70 uM DPB C17 H19 N2 O8 P CC1=CN(C(=....
6 2JAU - ATM C10 H14 N5 O7 P CC1=CN(C(=....
7 1Z4K - T3P C10 H15 N2 O8 P CC1=CN(C(=....
8 2JAW - BVP C11 H14 Br N2 O8 P C1[C@@H]([....
9 1Z4L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4L6C Ki = 2.71 uM 0BT C17 H18 I N2 O8 P CC1=CN(C(=....
11 1Z4Q - D4M C10 H13 N2 O7 P CC1=CN(C(=....
12 4MWO Ki = 7.9 uM 2E2 C18 H19 N2 O10 P CC1=CN(C(=....
13 1Z4I - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1Z4J - U2P C9 H13 N2 O9 P C1=CN(C(=O....
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1Q92 - DRM C10 H15 N2 O6 P C1C[C@H]([....
2 1Z4P - DGP C10 H14 N5 O7 P c1nc2c(n1[....
3 1Z4M - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4NFL Ki = 22.1 uM 2JW C17 H18 N3 O10 P CC1=CN(C(=....
5 1Q91 Ki = 70 uM DPB C17 H19 N2 O8 P CC1=CN(C(=....
6 2JAU - ATM C10 H14 N5 O7 P CC1=CN(C(=....
7 1Z4K - T3P C10 H15 N2 O8 P CC1=CN(C(=....
8 2JAW - BVP C11 H14 Br N2 O8 P C1[C@@H]([....
9 1Z4L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4L6C Ki = 2.71 uM 0BT C17 H18 I N2 O8 P CC1=CN(C(=....
11 1Z4Q - D4M C10 H13 N2 O7 P CC1=CN(C(=....
12 4MWO Ki = 7.9 uM 2E2 C18 H19 N2 O10 P CC1=CN(C(=....
13 1Z4I - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1Z4J - U2P C9 H13 N2 O9 P C1=CN(C(=O....
15 2JAR - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 2JAO - DGP C10 H14 N5 O7 P c1nc2c(n1[....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1Q92 - DRM C10 H15 N2 O6 P C1C[C@H]([....
2 1Z4P - DGP C10 H14 N5 O7 P c1nc2c(n1[....
3 1Z4M - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4NFL Ki = 22.1 uM 2JW C17 H18 N3 O10 P CC1=CN(C(=....
5 1Q91 Ki = 70 uM DPB C17 H19 N2 O8 P CC1=CN(C(=....
6 2JAU - ATM C10 H14 N5 O7 P CC1=CN(C(=....
7 1Z4K - T3P C10 H15 N2 O8 P CC1=CN(C(=....
8 2JAW - BVP C11 H14 Br N2 O8 P C1[C@@H]([....
9 1Z4L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4L6C Ki = 2.71 uM 0BT C17 H18 I N2 O8 P CC1=CN(C(=....
11 1Z4Q - D4M C10 H13 N2 O7 P CC1=CN(C(=....
12 4MWO Ki = 7.9 uM 2E2 C18 H19 N2 O10 P CC1=CN(C(=....
13 1Z4I - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1Z4J - U2P C9 H13 N2 O9 P C1=CN(C(=O....
15 2JAR - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 2JAO - DGP C10 H14 N5 O7 P c1nc2c(n1[....
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 : 4L6C; Ligand: 0BT; Similar sites found with APoc: 60
This union binding pocket(no: 1) in the query (biounit: 4l6c.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4IF4 BEF None
2 2FKA BEF None
3 3FGZ BEF None
4 6GR0 F8W None
5 4OWK NGA 1.44928
6 1YNS HPO 1.48515
7 4UMJ BFQ 1.48515
8 2QX0 PH2 1.88679
9 1RQL VSO 2.47525
10 3VPD CIT 2.47525
11 3UXH UXH 2.47525
12 3UXH FAD 2.47525
13 4ZEV M6P 2.47525
14 3QX9 ATP 2.89855
15 1G0H IPD 2.9703
16 3A1C ACP 2.9703
17 3L8G GMB 3.20856
18 4PPF FLC 3.46535
19 2WZF BGC 3.46535
20 2WPB ZZI 3.46535
21 6B8O PSF 3.5503
22 1L7N AF3 3.9604
23 5DX9 T6P 3.9604
24 5VLQ ANP 3.9604
25 4ZV1 ARG 3.9604
26 1L7N ALF 3.9604
27 1L7P SEP 3.9604
28 3BRE C2E 4.45545
29 1YHM AHD 4.45545
30 4UME KDO 4.66321
31 3F5A SIA GAL NAG 4.9505
32 2J8R MSL 5.23256
33 6BR7 BEF 5.26316
34 4HPP GLU 5.44554
35 2RBK VN4 5.94059
36 3OCZ SRA 5.94059
37 5L8N 6RQ 6.25
38 4CS9 AMP 6.34921
39 1Z4O GL1 6.43564
40 5FH7 5XL 6.45161
41 1L5Y BEF 7.09677
42 2HBL AMP 7.42574
43 5AHO TLA 7.42574
44 4PTN PYR 7.42574
45 4CCK OGA 7.42574
46 4K30 NLG 7.5
47 1Z5U CMP 7.92079
48 2P69 PLP 8.82353
49 3THR C2F 8.91089
50 5CGM MAL 9.40594
51 4OUJ LBT 9.90099
52 3EF0 ALF 10.8911
53 2FPU HSO 11.3636
54 4EXO PYR 12.3288
55 3K0T BGC 13.986
56 2YN4 39J 16.3366
57 5W3X ACO 17.3267
58 5W3Y ACO 17.3267
59 1TE2 PGA 17.8218
60 1QH9 LAC 27.2277
Pocket No.: 2; Query (leader) PDB : 4L6C; Ligand: 0BT; 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: 4l6c.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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