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
543.454 n/a P(=O)...
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 11 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 (57)
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 6XPV - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
40 6XPW - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
41 6XPU - IDP C10 H14 N4 O11 P2 c1nc2c(n1[....
42 6XPT - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
43 6XP7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 6XPS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
45 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
46 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
47 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
48 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
49 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
51 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
52 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
53 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
54 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
55 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
56 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
57 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GTP MG; Similar ligands found: 110
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP MG 1 1
2 GDP BEF 0.865854 0.973333
3 GDP ALF 0.816092 0.924051
4 GDP AF3 0.816092 0.924051
5 GDP 7MG 0.776596 0.948052
6 ALF 5GP 0.767442 0.924051
7 5GP 0.73494 0.972973
8 G 0.73494 0.972973
9 GDP 0.732558 0.96
10 GP3 0.72093 0.935065
11 GP2 0.712644 0.923077
12 GNH 0.704545 0.947368
13 G2P 0.692308 0.923077
14 GTP 0.688889 0.96
15 GMV 0.688889 0.935065
16 GCP 0.681319 0.935065
17 G1R 0.681319 0.947368
18 9GM 0.673913 0.935065
19 GSP 0.673913 0.911392
20 GNP 0.673913 0.935065
21 GAV 0.659574 0.923077
22 G2R 0.639175 0.923077
23 GMP 0.621951 0.866667
24 GPG 0.616162 0.923077
25 G1R G1R 0.612069 0.935897
26 Y9Z 0.607843 0.86747
27 GDD 0.607843 0.923077
28 GKE 0.607843 0.923077
29 GDC 0.607843 0.923077
30 PGD O 0.606838 0.83908
31 GDR 0.601942 0.923077
32 GTG 0.601942 0.924051
33 GFB 0.601942 0.923077
34 GKD 0.6 0.923077
35 YGP 0.598039 0.888889
36 6CK 0.596154 0.9
37 G3A 0.596154 0.935065
38 KB7 0.595745 0.8375
39 G5P 0.590476 0.935065
40 JB2 0.584906 0.923077
41 GPD 0.579439 0.888889
42 GDX 0.579439 0.935065
43 G3D 0.571429 0.946667
44 3GP 0.56044 0.933333
45 G4P 0.56 0.946667
46 I2C FE2 CMO CMO 0.559322 0.83908
47 JB3 0.553571 0.911392
48 FEG 0.548673 0.86747
49 NGD 0.548673 0.948052
50 ATP MG 0.547368 0.905405
51 ADP PO3 0.547368 0.905405
52 ZGP 0.54386 0.857143
53 KBD 0.538462 0.8375
54 0O2 0.538462 0.946667
55 U2G 0.535088 0.9
56 2MD 0.534483 0.857143
57 CAG 0.533898 0.869048
58 KBJ 0.53271 0.807229
59 MD1 0.528926 0.857143
60 CG2 0.525862 0.9
61 G C 0.521368 0.935897
62 MGD 0.521008 0.857143
63 M7G A2M G 0.517483 0.83908
64 2GP 0.510638 0.921053
65 TPG 0.508065 0.808989
66 PGD 0.504065 0.888889
67 DBG 0.496 0.911392
68 FE9 0.495935 0.784946
69 GTP 5GP 0.482456 0.934211
70 GPX 0.481132 0.907895
71 APC G U 0.48 0.922078
72 BEF ADP 0.48 0.881579
73 GH3 0.47619 0.934211
74 DGI 0.475248 0.886076
75 ADP BEF 0.474227 0.905405
76 ADP MG 0.474227 0.905405
77 BGO 0.470588 0.8875
78 G4M 0.470149 0.847059
79 P2G 0.469388 0.87013
80 ATP A A A 0.468468 0.893333
81 ATP A 0.468468 0.893333
82 P1G 0.46 0.858974
83 DGP 0.459184 0.897436
84 DG 0.459184 0.897436
85 AKW 0.458333 0.878049
86 DGT 0.457143 0.886076
87 IDP 0.455446 0.933333
88 VO4 ADP 0.451923 0.883117
89 IMP 0.44898 0.945946
90 GGM 0.447154 0.865854
91 QBQ 0.442308 0.946667
92 ALF ADP 0.438095 0.8375
93 5GP 5GP 0.432692 0.92
94 G7M 0.43 0.960526
95 G1G 0.429688 0.9125
96 SGP 0.425743 0.814815
97 R5I 0.424528 0.907895
98 R7I 0.424528 0.907895
99 PCG 0.423077 0.92
100 C2E 0.423077 0.907895
101 35G 0.423077 0.92
102 4TA 0.420635 0.8
103 OMC OMU OMG OMG U 0.41844 0.901235
104 AR6 AR6 0.415254 0.881579
105 GPC 0.414062 0.86747
106 ANP MG 0.411215 0.87013
107 MGP 0.411215 0.948052
108 PO4 PO4 A A A A PO4 0.410714 0.866667
109 ADP BMA 0.410714 0.858974
110 6G0 0.407407 0.948052
Similar Ligands (3D)
Ligand no: 1; Ligand: GTP MG; Similar ligands found: 3
No: Ligand Similarity coefficient
1 APC 0.8882
2 ADP 0.8843
3 ANP 0.8746
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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