Receptor
PDB id Resolution Class Description Source Keywords
3C3C 2.4 Å EC: 2.7.2.3 CRYSTAL STRUCTURE OF HUMAN PHOSPHOGLYCERATE KINASE BOUND TO 3-PHOSPHOGLYCERATE AND L-CDP HOMO SAPIENS PROTEIN-NUCLEOTIDE COMPLEX L-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
3PG A:418;
B:417;
Valid;
Valid;
none;
none;
submit data
186.057 C3 H7 O7 P C([C@...
CDP A:419;
Valid;
none;
submit data
403.176 C9 H15 N3 O11 P2 C1=CN...
MG A:417;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
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
Ligand no: 1; Ligand: 3PG; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 3PG 1 1
2 DER 0.575758 0.941176
3 DEZ 0.575758 0.941176
4 SEP 0.515152 0.74359
5 4TP 0.5 0.780488
6 PA5 0.486486 0.941176
7 R10 0.486486 0.941176
8 DG2 0.485714 0.909091
9 6PG 0.461538 0.941176
10 LG6 0.461538 0.941176
11 HG3 0.451613 0.9375
12 G3P 0.4375 0.852941
13 1GP 0.4375 0.852941
14 PGA 0.433333 0.90625
15 DXP 0.432432 0.911765
16 GOS 0.424242 0.857143
17 M2P 0.424242 0.857143
18 G3H 0.411765 0.9375
19 5RP 0.410256 0.837838
20 5SP 0.410256 0.837838
21 HMS 0.410256 0.837838
22 D5X 0.410256 0.941176
23 PEQ 0.40625 0.727273
24 0V5 0.40625 0.727273
25 XBP 0.4 0.885714
26 RUB 0.4 0.885714
27 RES 0.4 0.659574
Ligand no: 2; Ligand: CDP; Similar ligands found: 97
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 0RC 0.77027 0.918919
8 7XL 0.77027 0.944444
9 2TM 0.743243 0.958333
10 C2G 0.74026 0.957747
11 CDC 0.725 0.82716
12 C5G 0.707317 0.944444
13 CDM 0.695122 0.894737
14 CXY 0.678571 0.944444
15 CTN 0.636364 0.857143
16 AR3 0.636364 0.857143
17 C C C C 0.623529 0.916667
18 1AA 0.619565 0.906667
19 C C 0.607143 0.929577
20 UDP 0.605263 0.942029
21 I5A 0.602941 0.816901
22 YYY 0.582278 0.90411
23 GCQ 0.560976 0.90411
24 C3P 0.56 0.942857
25 MCN 0.557692 0.819277
26 PMT 0.554455 0.85
27 91P 0.553398 0.851852
28 UTP 0.54321 0.942029
29 2AA 0.542857 0.693878
30 16B 0.538462 0.917808
31 CSQ 0.536842 0.905405
32 CSV 0.536842 0.905405
33 U5F 0.536585 0.942029
34 DCP 0.535714 0.90411
35 GTF 0.523256 0.90411
36 C2P 0.519481 0.957143
37 PCD 0.517857 0.781609
38 FN5 0.509434 0.871795
39 GPC 0.509091 0.819277
40 CSF 0.504587 0.871795
41 DKZ 0.5 0.746667
42 HQ5 0.48913 0.758621
43 DCT 0.488372 0.90411
44 UNP 0.488372 0.915493
45 TKW 0.4875 0.971429
46 G C 0.481818 0.8375
47 5GW 0.477778 0.890411
48 5HM 0.47561 0.958333
49 YSC 0.469388 0.767442
50 A C A C 0.464912 0.835443
51 DC 0.463415 0.890411
52 DCM 0.463415 0.890411
53 U A C C 0.452174 0.846154
54 UPP 0.451613 0.888889
55 UDH 0.451613 0.844156
56 G8D 0.450549 0.907895
57 U5P 0.45 0.927536
58 U 0.45 0.927536
59 C5P SIA 0.447368 0.893333
60 GDU 0.446809 0.888889
61 URM 0.446809 0.876712
62 UFM 0.446809 0.888889
63 GUD 0.446809 0.888889
64 660 0.446809 0.876712
65 UPG 0.446809 0.888889
66 8OD 0.445652 0.855263
67 UPU 0.444444 0.887324
68 G G G C 0.444444 0.85
69 4GW 0.443299 0.866667
70 A G C C 0.440678 0.848101
71 DOC 0.439024 0.890411
72 M7G 0.43617 0.829268
73 U2F 0.43299 0.842105
74 UFG 0.43299 0.842105
75 UPF 0.43299 0.842105
76 2KH 0.431818 0.915493
77 G C C C 0.42623 0.860759
78 CG2 0.421053 0.873418
79 A U C C 0.420635 0.835443
80 G3N 0.42 0.890411
81 UDP UDP 0.418605 0.885714
82 UAD 0.418367 0.888889
83 UDX 0.418367 0.888889
84 44P 0.416667 0.902778
85 3UC 0.415842 0.842105
86 M7M 0.412371 0.797619
87 8GT 0.410526 0.907895
88 USQ 0.41 0.780488
89 UGB 0.41 0.901408
90 V12 0.41 0.75
91 UGA 0.41 0.901408
92 UP5 0.405405 0.857143
93 GEO 0.405063 0.783784
94 UDM 0.403846 0.864865
95 H6Y 0.402062 0.855263
96 NVG 0.401961 0.731707
97 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 : 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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