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Receptor
PDB id Resolution Class Description Source Keywords
2AZ3 2.2 Å EC: 2.7.4.6 STRUCTURE OF A HALOPHILIC NUCLEOSIDE DIPHOSPHATE KINASE FROM HALOBACTERIUM SALINARUM IN COMPLEX WITH CDP HALOBACTERIUM SALINARUM HALOPHILIC TRANSFERASE
Ref.: STRUCTURE OF A HALOPHILIC NUCLEOSIDE DIPHOSPHATE KI HALOBACTERIUM SALINARUM FEBS LETT. V. 579 6595 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CDP A:1100;
B:1200;
C:1300;
D:1400;
E:1500;
F:1600;
G:1700;
H:1800;
I:1900;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
MG A:201;
B:202;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2AZ3 2.2 Å EC: 2.7.4.6 STRUCTURE OF A HALOPHILIC NUCLEOSIDE DIPHOSPHATE KINASE FROM HALOBACTERIUM SALINARUM IN COMPLEX WITH CDP HALOBACTERIUM SALINARUM HALOPHILIC TRANSFERASE
Ref.: STRUCTURE OF A HALOPHILIC NUCLEOSIDE DIPHOSPHATE KI HALOBACTERIUM SALINARUM FEBS LETT. V. 579 6595 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2AZ3 - CDP C9 H15 N3 O11 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: CDP; Similar ligands found: 91
No: Ligand ECFP6 Tc MDL keys Tc
1 CDP 1 1
2 CTP 0.895522 1
3 HF4 0.895522 1
4 CAR 0.787879 0.985507
5 C 0.787879 0.985507
6 C5P 0.787879 0.985507
7 7XL 0.77027 0.944444
8 C2G 0.74026 0.957747
9 CDC 0.725 0.82716
10 C5G 0.707317 0.944444
11 CDM 0.695122 0.894737
12 CXY 0.678571 0.944444
13 CTN 0.636364 0.857143
14 AR3 0.636364 0.857143
15 C C C C 0.623529 0.916667
16 1AA 0.619565 0.906667
17 C C 0.607143 0.929577
18 UDP 0.605263 0.942029
19 I5A 0.602941 0.816901
20 YYY 0.582278 0.90411
21 GCQ 0.560976 0.90411
22 C3P 0.56 0.942857
23 MCN 0.557692 0.819277
24 PMT 0.554455 0.85
25 91P 0.553398 0.851852
26 UTP 0.54321 0.942029
27 2AA 0.542857 0.693878
28 16B 0.538462 0.917808
29 CSV 0.536842 0.905405
30 CSQ 0.536842 0.905405
31 DCP 0.535714 0.90411
32 GTF 0.523256 0.90411
33 C2P 0.519481 0.957143
34 PCD 0.517857 0.781609
35 FN5 0.509434 0.871795
36 GPC 0.509091 0.819277
37 CSF 0.504587 0.871795
38 DKZ 0.5 0.746667
39 UNP 0.488372 0.915493
40 TKW 0.4875 0.971429
41 G C 0.481818 0.8375
42 5GW 0.477778 0.890411
43 5HM 0.47561 0.958333
44 A C A C 0.464912 0.835443
45 DC 0.463415 0.890411
46 DCM 0.463415 0.890411
47 U A C C 0.452174 0.846154
48 UPP 0.451613 0.888889
49 UDH 0.451613 0.844156
50 G8D 0.450549 0.907895
51 U 0.45 0.927536
52 U5P 0.45 0.927536
53 C5P SIA 0.447368 0.893333
54 URM 0.446809 0.876712
55 660 0.446809 0.876712
56 GDU 0.446809 0.888889
57 UFM 0.446809 0.888889
58 GUD 0.446809 0.888889
59 UPG 0.446809 0.888889
60 8OD 0.445652 0.855263
61 G G G C 0.444444 0.85
62 UPU 0.444444 0.887324
63 4GW 0.443299 0.866667
64 A G C C 0.440678 0.848101
65 DOC 0.439024 0.890411
66 M7G 0.43617 0.829268
67 UFG 0.43299 0.842105
68 UPF 0.43299 0.842105
69 U2F 0.43299 0.842105
70 2KH 0.431818 0.915493
71 G C C C 0.42623 0.860759
72 CG2 0.421053 0.873418
73 A U C C 0.420635 0.835443
74 G3N 0.42 0.890411
75 UDP UDP 0.418605 0.885714
76 UAD 0.418367 0.888889
77 UDX 0.418367 0.888889
78 44P 0.416667 0.902778
79 3UC 0.415842 0.842105
80 M7M 0.412371 0.797619
81 8GT 0.410526 0.907895
82 V12 0.41 0.75
83 UGB 0.41 0.901408
84 USQ 0.41 0.780488
85 UGA 0.41 0.901408
86 UP5 0.405405 0.857143
87 GEO 0.405063 0.783784
88 UDM 0.403846 0.864865
89 H6Y 0.402062 0.855263
90 NVG 0.401961 0.731707
91 CTP C C C C 0.4 0.915493
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 17
This union binding pocket(no: 1) in the query (biounit: 2az3.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 5NW7 9C2 2.43902
2 1RWQ 5AP 3.04878
3 3P3G 3P3 3.04878
4 3P3G UKW 3.04878
5 5XWC 2IT 4.26829
6 5XWC NAP 4.26829
7 5XWC 8GL 4.26829
8 4Y7U 2KH 4.26829
9 2VMG MBG 5.09554
10 5U3B 7TD 6.70732
11 5GUD 2IT 7.31707
12 5GUD NDP 7.31707
13 1GQG DCD 7.31707
14 1QD1 FON 9.14634
15 2ZCQ B65 9.7561
16 3L0E G58 10.3659
17 3KFC 61X 10.3659
Pocket No.: 2; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 21
This union binding pocket(no: 2) in the query (biounit: 2az3.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 4QYN RTL 2.25564
2 5HIP 61O 3.04878
3 5NNA BZM 3.04878
4 5NG7 SER 3.65854
5 4X6X S74 3.65854
6 1E8G FAD 4.26829
7 3B9A NAG NAG NAG NAG NAG NAG 4.26829
8 1C7O PPG 4.26829
9 2Q3M MLA 4.87805
10 6F8B CXH 4.87805
11 5LXB 7A9 4.87805
12 3I54 CMP 4.87805
13 1G42 CP2 4.87805
14 5LJB RTL 5.18518
15 1EJB INJ 5.4878
16 3E2M E2M 5.4878
17 2P1M IHP 6.09756
18 1JR8 FAD 7.69231
19 4BVA T3 10.9756
20 6CEP NAD 10.9756
21 6GNF QPS 11.5854
Pocket No.: 3; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 4
This union binding pocket(no: 3) in the query (biounit: 2az3.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2BGS NDP 2.43902
2 3KYF 5GP 5GP 4.87805
3 1ZOA 140 7.31707
4 4X28 FDA 10.3659
Pocket No.: 4; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 2az3.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2VQ5 HBA 3.65854
2 4HXY NDP 4.87805
3 6CZ7 MGD 9.7561
Pocket No.: 5; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 1
This union binding pocket(no: 5) in the query (biounit: 2az3.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1GXS DKA 10.9756
Pocket No.: 6; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 14
This union binding pocket(no: 6) in the query (biounit: 2az3.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 5JU6 BGC 3.65854
2 5VHC BEF ADP 4.26829
3 2O07 MTA 5.4878
4 2O07 SPD 5.4878
5 2AHR NAP 5.4878
6 3ABA FLI 6.09756
7 2IHU TP9 6.70732
8 1OZH HE3 7.59717
9 4RQU NAD 7.92683
10 2OJW ADP 8.53659
11 3JVH HHV 10.3659
12 3OZ2 OZ2 11.5854
13 5K6N XYP 12.8049
14 2I7C AAT 15.2439
Pocket No.: 7; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 12
This union binding pocket(no: 7) in the query (biounit: 2az3.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1ONI BEZ None
2 2NVA PL2 3.04878
3 1XNG DND 3.04878
4 3VRV YSD 4.26829
5 2P1O IHP 6.09756
6 2P1O NLA 6.09756
7 4X6F 3XU 8.57143
8 5ECP JAA 10.3659
9 5ECP MET 10.3659
10 6CEP OXM 10.9756
11 4R5M 4NO 16.4634
12 4CYD CMP 19.0476
Pocket No.: 8; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2az3.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 1
This union binding pocket(no: 9) in the query (biounit: 2az3.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1OYJ GSH 4.26829
Pocket No.: 10; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 2az3.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: 3
This union binding pocket(no: 11) in the query (biounit: 2az3.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3WDM ADN 6.09756
2 4QCK ASD 7.92683
3 3HVJ 705 8.53659
Pocket No.: 12; Query (leader) PDB : 2AZ3; Ligand: CDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 2az3.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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