Receptor
PDB id Resolution Class Description Source Keywords
1BE4 2.4 Å EC: 2.7.4.6 NUCLEOSIDE DIPHOSPHATE KINASE ISOFORM B FROM BOVINE RETINA BOS TAURUS PHOSPHOTRANSFERASE
Ref.: NUCLEOSIDE DIPHOSPHATE KINASE FROM BOVINE RETINA: PURIFICATION, SUBCELLULAR LOCALIZATION, MOLECULAR C AND THREE-DIMENSIONAL STRUCTURE. BIOCHEMISTRY V. 37 13958 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PCG A:160;
B:160;
C:160;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
345.205 C10 H12 N5 O7 P c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1UCN 2 Å EC: 2.7.4.6 X-RAY STRUCTURE OF HUMAN NUCLEOSIDE DIPHOSPHATE KINASE A COM WITH ADP AT 2 A RESOLUTION HOMO SAPIENS MUTANT COMPLEXE ADP TRANSFERASE
Ref.: NUCLEOTIDE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE STRUCTURE OF HUMAN NDPK-A IN COMPLEX WITH ADP AND C TO PROTEIN KINASES J.MOL.BIOL. V. 332 915 2003
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
2 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
3 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
4 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
5 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
7 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 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 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 6XPV - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
17 6XPW - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
18 6XPU - IDP C10 H14 N4 O11 P2 c1nc2c(n1[....
19 6XPT - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
20 6XP7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 6XPS - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
22 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
23 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
25 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
26 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
27 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
28 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
30 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
31 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
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: PCG; Similar ligands found: 59
No: Ligand ECFP6 Tc MDL keys Tc
1 PCG 1 1
2 C2E 1 0.986111
3 35G 1 1
4 1YD 0.806818 0.986111
5 4BW 0.806818 0.986111
6 5GP 5GP 0.743902 0.945205
7 4UR 0.731959 0.986111
8 KT2 0.669903 0.986111
9 6SW 0.627907 0.957747
10 1YC 0.616162 0.958333
11 6J7 0.58427 0.946667
12 CMP 0.534091 0.888889
13 2BA 0.534091 0.902778
14 GMP 0.53012 0.84
15 1SY 0.495575 0.986111
16 SGP 0.483871 0.835443
17 6SZ 0.483871 0.902778
18 3GP 0.478261 0.932432
19 1OR 0.474747 0.729412
20 G 0.468085 0.945946
21 5GP 0.468085 0.945946
22 7CH 0.467391 0.875
23 6SX 0.462366 0.847222
24 6JR 0.457944 0.930556
25 G2R 0.457143 0.897436
26 GPX 0.451923 0.906667
27 GP3 0.44898 0.934211
28 2GP 0.446809 0.92
29 GP2 0.444444 0.897436
30 GDP 0.444444 0.933333
31 GNH 0.44 0.921053
32 KB7 0.44 0.790123
33 P2G 0.4375 0.893333
34 G2P 0.436893 0.897436
35 GMV 0.431373 0.909091
36 GTP 0.431373 0.933333
37 ALF 5GP 0.431373 0.851852
38 GDP BEF 0.427184 0.896104
39 G1R 0.427184 0.921053
40 GCP 0.427184 0.909091
41 GTP MG 0.423077 0.92
42 G3D 0.423077 0.945946
43 GNP 0.423077 0.909091
44 9GM 0.423077 0.909091
45 GSP 0.423077 0.886076
46 GDP AF3 0.420561 0.851852
47 G4P 0.415094 0.945946
48 GAV 0.415094 0.897436
49 P1G 0.414141 0.881579
50 KBD 0.412844 0.8125
51 Y9Z 0.410714 0.843373
52 GDP ALF 0.407407 0.851852
53 N6R 0.40708 0.818182
54 N6S 0.40708 0.818182
55 G3A 0.403509 0.934211
56 YGP 0.401786 0.8875
57 GPG 0.4 0.922078
58 0O2 0.4 0.945946
59 G5P 0.4 0.934211
Similar Ligands (3D)
Ligand no: 1; Ligand: PCG; Similar ligands found: 87
No: Ligand Similarity coefficient
1 75G 0.9865
2 SP1 0.9780
3 RP1 0.9758
4 6SY 0.9252
5 AMP 0.9201
6 DGP 0.9192
7 DG 0.9192
8 0NH 0.9188
9 CC7 0.9146
10 94M 0.9091
11 TMP 0.9018
12 NYM 0.9012
13 8OG 0.9006
14 UFP 0.9000
15 8MF 0.8998
16 71V 0.8945
17 ADN 0.8933
18 5F7 0.8915
19 5HM 0.8885
20 2DT 0.8880
21 D5M 0.8871
22 4UO 0.8870
23 5HU 0.8863
24 ZT2 0.8837
25 MG7 0.8829
26 9PP 0.8827
27 ACJ 0.8818
28 IXG 0.8818
29 NOJ BGC 0.8810
30 CHJ 0.8806
31 TOP 0.8786
32 HFS 0.8785
33 INI 0.8778
34 LU2 0.8776
35 0QX 0.8769
36 MTA 0.8760
37 8HG 0.8759
38 IMP 0.8751
39 6OG 0.8748
40 QTJ 0.8740
41 LRT 0.8739
42 9RK 0.8736
43 KMP 0.8733
44 D59 0.8732
45 AGI 0.8728
46 TYP 0.8726
47 2H4 0.8722
48 M77 0.8717
49 TCW 0.8714
50 147 0.8713
51 C4F 0.8712
52 UMP 0.8712
53 FDM 0.8702
54 CDY 0.8701
55 AX6 0.8699
56 3AM 0.8690
57 AJ8 0.8679
58 XYP XYP 0.8673
59 IXE 0.8663
60 AJ6 0.8661
61 XYP XYS 0.8659
62 5AD 0.8657
63 XYS XYS 0.8657
64 NXB 0.8655
65 3AD 0.8648
66 U5P 0.8636
67 KTM 0.8627
68 LOX XYP 0.8620
69 W72 0.8614
70 3WJ 0.8612
71 3WK 0.8610
72 8CS 0.8608
73 C5Q 0.8607
74 4L2 0.8607
75 9W8 0.8603
76 7FZ 0.8601
77 41L 0.8596
78 JA3 0.8593
79 E2N 0.8588
80 BGC BGC 0.8578
81 C 0.8573
82 69K 0.8568
83 MQ1 0.8564
84 H52 0.8558
85 FY8 0.8535
86 5YA 0.8534
87 PV0 0.8523
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1UCN; 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: 1ucn.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1UCN; 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: 1ucn.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1UCN; 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: 1ucn.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1UCN; 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: 1ucn.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1UCN; 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: 1ucn.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1UCN; 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: 1ucn.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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