Receptor
PDB id Resolution Class Description Source Keywords
3Q8V 2.5 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS NUCLEOSIDE DIPHOS KINASE COMPLEXED WITH UDP STAPHYLOCOCCUS AUREUS SUBSP. AUREUS FERRIDOXIN FOLD ALPHA-BETA PROTEIN FAMILY NUCLEOSIDE DIPHOKINASES (NDKS) A GAMMA PHOSPHATE NUCLEOSIDE TRIPHOSPHATESNUCLEOSIDE DIPHOSPHATE NUCLEOTIDE BINDING MAGNESIUM METABINDING PHOSPHORYLATION TRANSFERASE
Ref.: CONFORMATIONAL BASIS FOR SUBSTRATE RECOGNITION AND REGULATION OF CATALYTIC ACTIVITY IN STAPHYLOCOCCUS NUCLEOSIDE DI-PHOSPHATE KINASE. BIOCHIM.BIOPHYS.ACTA 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:159;
B:159;
D:159;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
UDP A:158;
B:158;
D:158;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
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: UDP; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 UPU 0.72973 0.940298
6 2KH 0.722222 0.970149
7 44P 0.720588 0.955882
8 URM 0.717949 0.927536
9 GUD 0.717949 0.941176
10 GDU 0.717949 0.941176
11 UFM 0.717949 0.941176
12 UPG 0.717949 0.941176
13 660 0.717949 0.927536
14 UDP UDP 0.714286 0.939394
15 UDH 0.705128 0.864865
16 UPP 0.705128 0.941176
17 UPF 0.691358 0.888889
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UDX 0.670732 0.941176
21 UAD 0.670732 0.941176
22 3UC 0.658824 0.888889
23 USQ 0.654762 0.820513
24 UGB 0.654762 0.955224
25 UGA 0.654762 0.955224
26 G3N 0.647059 0.914286
27 UDM 0.636364 0.914286
28 URI 0.625 0.863636
29 U 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 UDP GAL 0.611765 0.913043
33 Y6W 0.607143 0.888889
34 CDP 0.605263 0.942029
35 UD7 0.591398 0.927536
36 HP7 0.591398 0.941176
37 MJZ 0.585106 0.914286
38 IUG 0.583333 0.810127
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 UD4 0.578947 0.914286
42 CJB 0.573529 0.820895
43 UDZ 0.571429 0.853333
44 DUD 0.571429 0.913043
45 UP5 0.571429 0.853333
46 U U 0.563218 0.955224
47 EPZ 0.56 0.914286
48 5GW 0.559524 0.942029
49 EPU 0.554455 0.901408
50 EEB 0.554455 0.901408
51 UA3 0.547945 0.939394
52 U3P 0.547945 0.939394
53 CH 0.546667 0.913043
54 4TC 0.544554 0.831169
55 CTP 0.54321 0.942029
56 CSV 0.531915 0.851351
57 CSQ 0.531915 0.851351
58 DUT 0.52439 0.913043
59 4GW 0.516484 0.915493
60 UMA 0.513761 0.914286
61 U4S 0.513158 0.753425
62 U2P 0.506667 0.954545
63 U2S 0.5 0.767123
64 U3S 0.5 0.753425
65 PUP 0.48913 0.913043
66 U22 0.486957 0.790123
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 DKX 0.486486 0.746479
70 U1S 0.482759 0.75
71 A U 0.481132 0.805195
72 2QR 0.478632 0.822785
73 5FU 0.474359 0.914286
74 8OD 0.47191 0.851351
75 C5G 0.468085 0.888889
76 7XL 0.465909 0.888889
77 U U U U 0.461538 0.940298
78 UMF 0.461538 0.857143
79 G8D 0.460674 0.855263
80 UTP U U U 0.456522 0.895522
81 2TU 0.452055 0.774648
82 4RA 0.451613 0.855263
83 C2G 0.450549 0.901408
84 DU 0.45 0.898551
85 CAR 0.45 0.927536
86 C 0.45 0.927536
87 C5P 0.45 0.927536
88 UMP 0.45 0.898551
89 UAG 0.448 0.864865
90 CDC 0.446809 0.777778
91 UD0 0.444444 0.844156
92 5BU 0.444444 0.914286
93 N3E 0.440476 0.733333
94 UC5 0.440476 0.9
95 UUA 0.438356 0.772727
96 DUP 0.431818 0.887324
97 2GW 0.431373 0.901408
98 M7G 0.430108 0.780488
99 CNU 0.428571 0.927536
100 CDM 0.427083 0.842105
101 H6Y 0.425532 0.851351
102 16B 0.421687 0.888889
103 S5P 0.419753 0.915493
104 8GT 0.419355 0.855263
105 CXY 0.418367 0.888889
106 UPA 0.418182 0.842105
107 CDP MG 0.413793 0.849315
108 U2G 0.410714 0.822785
109 U A A U 0.409836 0.842105
110 UML 0.408759 0.810127
111 UP6 0.407407 0.871429
112 M7M 0.40625 0.771084
113 PMP UD1 0.404762 0.794872
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found: 17
This union binding pocket(no: 2) in the query (biounit: 3q8u.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4QYN RTL 0.01444 0.4188 None
2 5LJB RTL 0.01892 0.40897 None
3 3CH6 311 0.03009 0.43604 2.54777
4 3CH6 NAP 0.03009 0.43604 2.54777
5 1GS5 NLG 0.0206 0.4246 2.54777
6 3B9A NAG NAG NAG NAG NAG NAG 0.04231 0.40336 2.54777
7 5NB7 8NQ 0.0153 0.41588 3.18471
8 2Q3M MLA 0.004976 0.43091 4.4586
9 4NKW PLO 0.01868 0.40975 5.09554
10 3AI7 TPP 0.03081 0.40711 5.09554
11 4BVM VCA 0.026 0.40538 5.26316
12 4BVM PLM 0.0287 0.40167 5.26316
13 4X28 FDA 0.007128 0.4467 6.36943
14 1GXS DKA 0.009136 0.40695 8.28025
15 4X6X S74 0.007432 0.43289 8.9172
16 3QF7 ANP 0.04468 0.40267 8.9172
17 1ZAP A70 0.03551 0.40703 12.1019
Pocket No.: 3; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found: 4
This union binding pocket(no: 5) in the query (biounit: 3q8u.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5K6N XYP 0.01544 0.40023 3.18471
2 1G42 CP2 0.0166 0.40342 3.82166
3 1FQ5 0GM 0.04106 0.40119 4.4586
4 1UNH IXM 0.01833 0.40352 11.465
Pocket No.: 6; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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