Receptor
PDB id Resolution Class Description Source Keywords
3Q86 2.38 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS NUCLEOSIDE DIPHOS KINASE COMPLEXED WITH GTP STAPHYLOCOCCUS AUREUS SUBSP. AUREUS FERRIDOXIN FOLD ALPHA-BETA PROTEIN FAMILY NUCLEOSIDE DIPHOKINASES (NDKS) TRANSFER A GAMMA PHOSPHATE NUCLEOSIDE TRIPHOSPHATES NUCLEOSIDE DIPHOSPHATE NUCLEOTIDE BINDING MMETAL BINDING PHOSPHORYLATION TRANSFERASE
Ref.: CONFORMATIONAL BASIS FOR SUBSTRATE RECOGNITION AND REGULATION OF CATALYTIC ACTIVITY IN STAPHYLOCOCCUS NUCLEOSIDE DI-PHOSPHATE KINASE. BIOCHIM.BIOPHYS.ACTA V.1814 1349 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GTP MG A:158;
B:158;
Valid;
Valid;
none;
none;
submit data n/a n/a n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3Q8U 2.22 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS NUCLEOSIDE DIPHOS KINASE COMPLEXED WITH ADP STAPHYLOCOCCUS AUREUS SUBSP. AUREUS FERRIDOXIN FOLD ALPHA-BETA PROTEIN FAMILY NUCLEOSIDE DIPHOKINASES (NDKS) CATALYZE THE TRANSFER OF A GAMMA PHOSPHATE FNUCLEOSIDE TRIPHOSPHATES TO NUCLEOSIDE DIPHOSPHATE NUCLEOTBINDING MAGNESIUM METAL BINDING PHOSPHORYLATION TRANSFE
Ref.: CONFORMATIONAL BASIS FOR SUBSTRATE RECOGNITION AND REGULATION OF CATALYTIC ACTIVITY IN STAPHYLOCOCCUS NUCLEOSIDE DI-PHOSPHATE KINASE. BIOCHIM.BIOPHYS.ACTA V.1814 1349 2011
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 3Q86 - GTP MG n/a n/a
2 3Q8U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3Q8V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3Q86 - GTP MG n/a n/a
2 3Q8U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3Q8V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
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: GTP MG; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3Q8U; 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: 1) in the query (biounit: 3q8u.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3Q8U; 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: 3q8u.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3Q8U; 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: 3) in the query (biounit: 3q8u.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3Q8U; 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: 3q8u.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3Q8U; 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: 5) in the query (biounit: 3q8u.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3Q8U; 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: 6) in the query (biounit: 3q8u.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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