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Receptor
PDB id Resolution Class Description Source Keywords
1NHK 1.9 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE S UBSTRATE AT 2.0 ANGSTROMS RESOLUTION MYXOCOCCUS XANTHUS PHOSPHOTRANSFERASE
Ref.: THE 1.9 A CRYSTAL STRUCTURE OF A NUCLEOSIDE DIPHOSPHATE KINASE COMPLEX WITH ADENOSINE 3',5'-CYCLIC MONOPHOSPHATE: EVIDENCE FOR COMPETITIVE INHIBITION. J.MOL.BIOL. V. 249 665 1995
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CMP L:146;
R:1;
Valid;
Valid;
none;
none;
submit data
329.206 C10 H12 N5 O6 P c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1NHK 1.9 Å EC: 2.7.4.6 CRYSTAL STRUCTURE OF MYXOCOCCUS XANTHUS NUCLEOSIDE DIPHOSPHATE KINASE AND ITS INTERACTION WITH A NUCLEOTIDE S UBSTRATE AT 2.0 ANGSTROMS RESOLUTION MYXOCOCCUS XANTHUS PHOSPHOTRANSFERASE
Ref.: THE 1.9 A CRYSTAL STRUCTURE OF A NUCLEOSIDE DIPHOSPHATE KINASE COMPLEX WITH ADENOSINE 3',5'-CYCLIC MONOPHOSPHATE: EVIDENCE FOR COMPETITIVE INHIBITION. J.MOL.BIOL. V. 249 665 1995
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
2 1NLK - 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: CMP; Similar ligands found: 93
No: Ligand ECFP6 Tc MDL keys Tc
1 2BA 1 0.984848
2 CMP 1 1
3 RP1 0.757143 0.928571
4 SP1 0.757143 0.928571
5 1YD 0.727273 0.902778
6 4BW 0.727273 0.902778
7 1SY 0.653061 0.902778
8 1OR 0.635294 0.807692
9 4UR 0.626263 0.902778
10 7CH 0.580247 0.984615
11 6SX 0.573171 0.953846
12 6SZ 0.559524 0.984848
13 N6R 0.535354 0.914286
14 N6S 0.535354 0.914286
15 PCG 0.534091 0.888889
16 35G 0.534091 0.888889
17 C2E 0.534091 0.902778
18 1YC 0.53 0.875
19 Y3J 0.506667 0.753623
20 XYA 0.5 0.826087
21 5CD 0.5 0.811594
22 ACK 0.5 0.897059
23 RAB 0.5 0.826087
24 ADN 0.5 0.826087
25 6SW 0.494382 0.9
26 5AD 0.493151 0.776119
27 5N5 0.486842 0.8
28 75G 0.483146 0.890411
29 A4D 0.480519 0.8
30 M2T 0.475 0.736842
31 MTA 0.469136 0.777778
32 CC5 0.466667 0.850746
33 EP4 0.4625 0.756757
34 DTA 0.45679 0.816901
35 QQX 0.452381 0.835616
36 LMS 0.447059 0.7875
37 AMP 0.447059 0.927536
38 QQY 0.447059 0.847222
39 A 0.447059 0.927536
40 3DH 0.440476 0.777778
41 3AM 0.435294 0.913043
42 A2D 0.431818 0.928571
43 J7C 0.431818 0.75
44 ABM 0.431818 0.901408
45 ZAS 0.430233 0.77027
46 7D7 0.428571 0.771429
47 S4M 0.426966 0.666667
48 SRA 0.425287 0.876712
49 6RE 0.425287 0.74026
50 3AD 0.425 0.838235
51 2AM 0.423529 0.9
52 BA3 0.422222 0.928571
53 A12 0.422222 0.864865
54 AP2 0.422222 0.864865
55 MAO 0.422222 0.740741
56 DSH 0.420455 0.727273
57 NEC 0.420455 0.726027
58 AOC 0.420455 0.802817
59 A3G 0.420455 0.780822
60 SFG 0.419355 0.753425
61 6JR 0.419048 0.927536
62 ADP 0.417582 0.901408
63 AP5 0.417582 0.928571
64 5AS 0.417582 0.741176
65 B4P 0.417582 0.928571
66 A3N 0.41573 0.767123
67 APC 0.414894 0.864865
68 AN2 0.413043 0.888889
69 SON 0.413043 0.864865
70 AT4 0.413043 0.864865
71 EEM 0.412371 0.691358
72 GJV 0.411111 0.730769
73 GGZ 0.41 0.78481
74 OVE 0.409091 0.863014
75 M33 0.408602 0.888889
76 ADX 0.408602 0.810127
77 AU1 0.408602 0.876712
78 CA0 0.408602 0.876712
79 A3P 0.406593 0.927536
80 5X8 0.404255 0.767123
81 ATP 0.404255 0.901408
82 ACP 0.404255 0.876712
83 HEJ 0.404255 0.901408
84 50T 0.404255 0.888889
85 ADP VO4 0.40404 0.888889
86 VO4 ADP 0.40404 0.888889
87 SAM 0.402062 0.691358
88 0UM 0.401961 0.7
89 AR6 0.4 0.901408
90 AQP 0.4 0.901408
91 5FA 0.4 0.901408
92 APR 0.4 0.901408
93 PRX 0.4 0.876712
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NHK; Ligand: CMP; Similar sites found with APoc: 14
This union binding pocket(no: 1) in the query (biounit: 1nhk.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 2H29 DND 2.08333
2 2QTR NXX 3.47222
3 5NNA BZM 4.16667
4 5LWY OLB 4.6729
5 5GM9 CBI 4.86111
6 2ZA5 2FF 4.86111
7 2IHU TP9 7.63889
8 3DER ALA LYS 8.33333
9 2HJR APR 8.33333
10 4M37 SAH 9.02778
11 1NF8 BOG 9.72222
12 1I0B PEL 9.72222
13 5LJI FMN 13.8889
14 3MA0 XYP 15.9722
Pocket No.: 2; Query (leader) PDB : 1NHK; Ligand: CMP; 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: 1nhk.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1NHK; Ligand: CMP; Similar sites found with APoc: 5
This union binding pocket(no: 3) in the query (biounit: 1nhk.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4OJ8 2TQ 3.47222
2 4OJ8 AKG 3.47222
3 6CEP NAD 6.25
4 6CEP OXM 6.25
5 4X28 FDA 18.0556
Pocket No.: 4; Query (leader) PDB : 1NHK; Ligand: CMP; 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: 1nhk.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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