Receptor
PDB id Resolution Class Description Source Keywords
3C3B 1.8 Å EC: 2.7.2.3 CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE BOUND TO D-CDP HOMO SAPIENS PROTEIN-NUCLEOTIDE COMPLEX D-ENANTIOMER OF CDP KINASE ACETYLATION ATP-BINDING CYTOPLASM DISEASE MUTATION GLYCOLYSIS HEREDITARY HEMOLYTIC ANEMIA NUCLEOTIDE-BINDINGPHOSPHOPROTEIN POLYMORPHISM TRANSFERASE
Ref.: MOLECULAR BASIS FOR THE LACK OF ENANTIOSELECTIVITY OF HUMAN 3-PHOSPHOGLYCERATE KINASE NUCLEIC ACIDS RES. V. 36 3620 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CDP B:418;
 Valid;
 none;
 submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
PO4 A:417;
B:417;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4O33 2.1 Å EC: 2.7.2.3 CRYSTAL STRUCTURE OF HUMAN PGK1 3PG AND TERAZOSIN(TZN) TERNA HOMO SAPIENS ENZYME-DRUG COMPLEX TRANSFERASE-TRANSFERASE ACTIVITOR COMPLTRANSFERASE-TRANSFERASE ACTIVATOR COMPLEX
Ref.: TERAZOSIN ACTIVATES PGK1 AND HSP90 TO PROMOTE STRES RESISTANCE. NAT.CHEM.BIOL. V. 11 19 2015
Members (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5O7D - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 2WZC - ALF ADP 3PG n/a n/a
3 5M3U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
5 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
7 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
8 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
10 5M1R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
12 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
14 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
15 5MXM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
17 2WZD - AF3 ADP 3PG n/a n/a
18 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
19 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
20 2YBE - LA8 ALF 3PG n/a n/a
21 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
22 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
23 5M6Z - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
2 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
3 5O7D - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 2WZC - ALF ADP 3PG n/a n/a
5 5M3U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
6 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
7 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
8 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
9 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
10 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
12 5M1R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
13 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
16 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
17 5MXM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 2WZD - AF3 ADP 3PG n/a n/a
20 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
21 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
22 2YBE - LA8 ALF 3PG n/a n/a
23 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
24 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
25 5M6Z - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
26 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
50% Homology Family (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 13PK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
2 16PK - BIS C15 H22 F4 N5 O12 P3 c1nc(c2c(n....
3 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
4 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
5 2CUN - 3PG C3 H7 O7 P C([C@H](C(....
6 5O7D - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
7 2WZC - ALF ADP 3PG n/a n/a
8 5M3U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
9 1HDI - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2XE7 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 3C3B - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
12 4O3F Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
13 3C3A - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1KF0 Kd = 2.8 mM ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
15 5M1R - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 2ZGV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
17 2WZB - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1VJD Kd = 0.286 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
19 3C3C - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
20 5MXM - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 1VJC Kd = 0.263 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
22 2WZD - AF3 ADP 3PG n/a n/a
23 3C39 - 3PG C3 H7 O7 P C([C@H](C(....
24 2XE8 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
25 2YBE - LA8 ALF 3PG n/a n/a
26 2XE6 - 3PG C3 H7 O7 P C([C@H](C(....
27 4O33 Kd = 2.78 uM TZN C19 H25 N5 O4 COc1cc2c(c....
28 5M6Z - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 2P9T - 3PG C3 H7 O7 P C([C@H](C(....
30 6HXE - 3PG C3 H7 O7 P C([C@H](C(....
31 1VPE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
32 1PHP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
33 3ZLB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: CDP; Similar ligands found: 100
No: Ligand ECFP6 Tc MDL keys Tc
1 CDP 1 1
2 HF4 0.895522 1
3 CTP 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 0RC 0.77027 0.918919
9 2TM 0.743243 0.958333
10 C2G 0.74026 0.957747
11 CDC 0.725 0.82716
12 CDP MG 0.722222 0.942857
13 C5G 0.707317 0.944444
14 CDM 0.695122 0.894737
15 CXY 0.678571 0.944444
16 AR3 0.636364 0.857143
17 CTN 0.636364 0.857143
18 1AA 0.619565 0.906667
19 A7R 0.606383 0.931507
20 UDP 0.605263 0.942029
21 I5A 0.602941 0.816901
22 YYY 0.582278 0.90411
23 CDP RB0 0.577778 0.917808
24 GCQ 0.560976 0.90411
25 C3P 0.56 0.942857
26 MCN 0.557692 0.819277
27 PMT 0.554455 0.85
28 91P 0.553398 0.851852
29 UTP 0.54321 0.942029
30 2AA 0.542857 0.693878
31 16B 0.538462 0.917808
32 CSV 0.536842 0.905405
33 CSQ 0.536842 0.905405
34 U5F 0.536585 0.942029
35 DCP 0.535714 0.90411
36 GTF 0.523256 0.90411
37 C2P 0.519481 0.957143
38 PCD 0.517857 0.781609
39 FZQ 0.511364 0.797619
40 FN5 0.509434 0.871795
41 GPC 0.509091 0.819277
42 CSF 0.504587 0.871795
43 DKZ 0.5 0.746667
44 NCC 0.495413 0.918919
45 HQ5 0.48913 0.758621
46 UNP 0.488372 0.915493
47 DCT 0.488372 0.90411
48 TKW 0.4875 0.971429
49 G G 6MZ C 0.486239 0.814815
50 G C 0.481818 0.8375
51 5GW 0.477778 0.890411
52 5HM 0.47561 0.958333
53 BUP 0.471264 0.878378
54 YSC 0.469388 0.767442
55 DCM 0.463415 0.890411
56 DC 0.463415 0.890411
57 UPP 0.451613 0.888889
58 UDH 0.451613 0.844156
59 G8D 0.450549 0.907895
60 U 0.45 0.927536
61 U5P 0.45 0.927536
62 C5P SIA 0.447368 0.893333
63 660 0.446809 0.876712
64 UFM 0.446809 0.888889
65 GDU 0.446809 0.888889
66 URM 0.446809 0.876712
67 UPG 0.446809 0.888889
68 8OD 0.445652 0.855263
69 0KX 0.444444 0.88
70 UPU 0.444444 0.887324
71 4GW 0.443299 0.866667
72 DOC 0.439024 0.890411
73 M7G 0.43617 0.829268
74 U2F 0.43299 0.842105
75 UFG 0.43299 0.842105
76 UPF 0.43299 0.842105
77 2KH 0.431818 0.915493
78 AWU 0.427083 0.888889
79 CG2 0.421053 0.873418
80 G3N 0.42 0.890411
81 UDP UDP 0.418605 0.885714
82 UDX 0.418367 0.888889
83 UAD 0.418367 0.888889
84 44P 0.416667 0.902778
85 3UC 0.415842 0.842105
86 DCP MG 0.413043 0.851351
87 M7M 0.412371 0.797619
88 8GT 0.410526 0.907895
89 V12 0.41 0.75
90 UGB 0.41 0.901408
91 UGA 0.41 0.901408
92 USQ 0.41 0.780488
93 UGF 0.405941 0.853333
94 UP5 0.405405 0.857143
95 GEO 0.405063 0.783784
96 UDM 0.403846 0.864865
97 H6Y 0.402062 0.855263
98 NVG 0.401961 0.731707
99 CTP C C C C 0.4 0.915493
100 6MZ C U 0.4 0.814815
Similar Ligands (3D)
Ligand no: 1; Ligand: CDP; Similar ligands found: 38
No: Ligand Similarity coefficient
1 DUD 0.9790
2 TBD 0.9634
3 TYD 0.9611
4 ADP 0.9333
5 D4D 0.9313
6 DUN 0.9274
7 ADX 0.9253
8 IDP 0.9252
9 BEF ADP 0.9235
10 AU1 0.9225
11 AN2 0.9215
12 ADP MG 0.9194
13 UMP 0.9193
14 AP2 0.9182
15 A12 0.9182
16 DGI 0.9158
17 M33 0.9122
18 CUU 0.9102
19 GDP 0.9093
20 AMP 0.9080
21 U3S 0.9071
22 DAT 0.9016
23 TMP 0.8942
24 U1S 0.8914
25 CH 0.8874
26 H2U 0.8816
27 2A5 0.8762
28 DU 0.8746
29 SON 0.8726
30 SSA 0.8707
31 AZD 0.8684
32 7D3 0.8672
33 T3S 0.8656
34 DDN 0.8643
35 DUT 0.8631
36 AMZ 0.8619
37 C8M 0.8613
38 BMP 0.8569
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4O33; Ligand: TZN; 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: 4o33.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4O33; Ligand: 3PG; 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: 4o33.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
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