-->
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: 117
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 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
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: 24
This union binding pocket(no: 1) in the query (biounit: 3q8u.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 5O42 NAD 2.54777
2 5O42 BGC 2.54777
3 5O42 9JW 2.54777
4 5JU6 BGC 3.18471
5 5K6N XYP 3.18471
6 5NB7 8NQ 3.18471
7 6GNF QPS 3.18471
8 4IID NOJ 3.82166
9 3GGO NAI 4.4586
10 3GGO ENO 4.4586
11 2Q3M MLA 4.4586
12 1OZH HE3 4.4586
13 4NKW PLO 5.09554
14 1MEX RAC 5.09554
15 3WN0 FUB 6.36943
16 1ZOA 140 7.00637
17 2IHU TP9 7.00637
18 5U3B 7TD 7.00637
19 1O2D NAP 9.55414
20 5X1M DHB 12.7389
21 4R2M ANP 15.2866
22 1RV0 NDG 17.8344
23 1RV0 DAN 17.8344
24 3AJH BL3 22.9299
Pocket No.: 2; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 3q8u.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 5LJB RTL None
2 3CH6 NAP 2.54777
3 3CH6 311 2.54777
4 1GS5 NLG 2.54777
5 1GS5 ANP 2.54777
6 3B9A NAG NAG NAG NAG NAG NAG 2.54777
7 2UXI G50 3.82166
8 5YVR NDP 4.4586
9 3AI7 TPP 5.09554
10 4BVM VCA 5.26316
11 4BVM PLM 5.26316
12 4X28 FDA 6.36943
13 4JTA NAP 7.64331
14 6HLX G9Z 7.64331
15 1GXS DKA 8.28025
16 4X6X S74 8.9172
17 3QF7 ANP 8.9172
18 6CEP OXM 10.1911
19 1E8G FCR 12.1019
20 1ZAP A70 12.1019
Pocket No.: 3; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found with APoc: 15
This union binding pocket(no: 3) in the query (biounit: 3q8u.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 4QYN RTL None
2 1JR8 FAD None
3 5HZ9 5M8 None
4 4RFR RHN 1.27389
5 5NW7 9C2 2.54777
6 4R6W SAH 3.18471
7 2BP1 NDP 5.09554
8 1R6T TYM 7.64331
9 3PP0 03Q 7.64331
10 5UXH GFB 7.64331
11 2C91 NAP 11.465
12 1UNH IXM 11.465
13 5X1M THG 12.7389
14 3HVJ 705 17.1975
15 1ESM COA 19.7452
Pocket No.: 4; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found with APoc: 4
This union binding pocket(no: 4) in the query (biounit: 3q8u.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 6ALW BNV None
2 6ALW BMJ None
3 4NG2 OHN 2.54777
4 3D36 ADP 5.09554
Pocket No.: 5; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found with APoc: 6
This union binding pocket(no: 5) in the query (biounit: 3q8u.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1G42 CP2 3.82166
2 1FQ5 0GM 4.4586
3 1SUW NAP 4.4586
4 1A78 TDG 5.22388
5 5EYG NAP 5.73248
6 5K8P 6R8 7.00637
Pocket No.: 6; Query (leader) PDB : 3Q8U; Ligand: ADP; Similar sites found with APoc: 14
This union binding pocket(no: 6) in the query (biounit: 3q8u.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 3E2M E2M None
2 1A05 IPM 1.27389
3 3JZB 4HY 4.4586
4 6AMI TRP 5.73248
5 1KBJ FMN 5.73248
6 2IUW AKG 7.00637
7 5G4J EXT 7.64331
8 3ZDS OMD 8.28025
9 3O9L LPN 8.28025
10 4NST ADP 8.9172
11 5HQ0 LZ9 11.465
12 4RPO T6C 12.7389
13 4KWI NAP 17.8344
14 4KQI RBZ 22.293
APoc FAQ
Feedback