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Receptor
PDB id Resolution Class Description Source Keywords
4UOG 2.3 Å EC: 2.7.4.6 CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM LITOPENAEUS VANNAMEI COMPLEXED WITH DCDP LITOPENAEUS VANNAMEI TRANSFERASE BINARY COMPLEX DCDP PYRIMIDINE BINDING SITEDESOXYNUCLEOTIDE
Ref.: STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM PAC SHRIMP (LITOPENAEUS VANNAMEI) IN BINARY COMPLEXES W PURINE AND PYRIMIDINE NUCLEOSIDE DIPHOSPHATES ACTA CRYSTALLOGR.,SECT.F V. 79 1150 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
YYY A:1152;
C:1152;
B:1152;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
387.177 C9 H15 N3 O10 P2 C1[C@...
MG A:1153;
B:1153;
C:1153;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4UOH 2.01 Å EC: 2.7.4.6 CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM LITOPENAEUS VANNAMEI COMPLEXED WITH ADP LITOPENAEUS VANNAMEI TRANSFERASE BINARY COMPLEX ADP PURINE WHITE-SHRIMP BINSITE NUCLEOTIDE
Ref.: STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM PAC SHRIMP (LITOPENAEUS VANNAMEI) IN BINARY COMPLEXES W PURINE AND PYRIMIDINE NUCLEOSIDE DIPHOSPHATES ACTA CRYSTALLOGR.,SECT.F V. 79 1150 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
2 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
17 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
19 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
20 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
22 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (51)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3EVO - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
14 3ELH - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
15 3GP9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3EJM - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 3FBB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
18 3EMT - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
19 3FCV - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
20 3EIC - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
21 3EVM - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
22 3B6B - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
23 3FCW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
24 2B8Q - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
25 3DKD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
26 3DDI - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
27 3FBE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
28 3ETM - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
29 3GPA - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
30 3ENA - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
31 3EM1 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
32 3EE3 - CDP MG n/a n/a
33 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 3Q86 - GTP MG n/a n/a
35 3Q8U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 3Q8V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
37 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
38 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
39 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
40 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
42 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
43 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
45 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
46 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
47 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
48 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
51 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YYY; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 YYY 1 1
2 DCP 0.884058 1
3 DC 0.80597 0.985714
4 DCM 0.80597 0.985714
5 DCZ 0.641791 0.847222
6 LDC 0.641791 0.847222
7 DUD 0.589744 0.929577
8 CDP 0.582278 0.90411
9 GCQ 0.554217 0.891892
10 TYD 0.536585 0.891892
11 CTP 0.52381 0.90411
12 HF4 0.52381 0.90411
13 DUT 0.52381 0.929577
14 GTF 0.5 0.891892
15 DOC 0.4875 0.957747
16 CPA 0.485981 0.85
17 8GD 0.483516 0.875
18 6U4 0.478723 0.921053
19 TTP 0.477273 0.891892
20 CGP 0.468468 0.841463
21 7XL 0.466667 0.88
22 8DD 0.457447 0.835443
23 C 0.451219 0.890411
24 DU 0.451219 0.915493
25 C5P 0.451219 0.890411
26 UMP 0.451219 0.915493
27 CAR 0.451219 0.890411
28 CXY 0.44898 0.88
29 CDC 0.447917 0.77381
30 DG DC 0.441667 0.851852
31 C2G 0.43617 0.891892
32 DUP 0.433333 0.90411
33 8DG 0.43299 0.875
34 CDM 0.428571 0.858974
35 DC DG 0.426087 0.819277
36 C5G 0.424242 0.855263
37 DDN 0.421687 0.915493
38 C2P 0.421687 0.916667
39 C3P 0.421687 0.876712
40 UFP 0.411765 0.855263
41 LTT 0.410256 0.77027
42 UC5 0.409091 0.916667
43 DAT 0.408602 0.831169
44 TMP 0.406977 0.878378
45 BRU 0.406977 0.855263
46 DGI 0.40625 0.848101
47 3TC 0.405063 0.76
48 TLO 0.40404 0.844156
49 0FX 0.4 0.835443
50 DUN 0.4 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UOH; Ligand: ADP; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 4uoh.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 3V49 PK0 None
2 6FE1 V14 3.31126
3 2HFN FMN 3.97351
4 4X28 FDA 4.63576
5 1RM6 PCD 5.96026
6 2IOY RIP 6.62252
7 1DRJ RIP 7.28477
Pocket No.: 2; Query (leader) PDB : 4UOH; Ligand: ADP; 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: 4uoh.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4UOH; Ligand: ADP; Similar sites found with APoc: 5
This union binding pocket(no: 3) in the query (biounit: 4uoh.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJK TPP 5.29801
2 1GXS DKA 5.96026
3 5OKG BG6 5.96026
4 3QDW A2G 6.99301
5 3QDV A2G 6.99301
Pocket No.: 4; Query (leader) PDB : 4UOH; Ligand: ADP; 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: 4uoh.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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