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Receptor
PDB id Resolution Class Description Source Keywords
3PGK 2.5 Å EC: 2.7.2.3 THE STRUCTURE OF YEAST PHOSPHOGLYCERATE KINASE AT 0.25 NM RE SACCHAROMYCES CEREVISIAE PHOSPHOTRANSFERASE(CARBOXYL AS ACCEPTOR) TRANSFERASE
Ref.: SEQUENCE AND STRUCTURE OF YEAST PHOSPHOGLYCERATE KI EMBO J. V. 1 1635 1982
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PG A:418;
Valid;
none;
submit data
186.057 C3 H7 O7 P C([C@...
ATP A:417;
Invalid;
none;
submit data
507.181 C10 H16 N5 O13 P3 c1nc(...
MG A:416;
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
1QPG 2.4 Å EC: 2.7.2.3 3-PHOSPHOGLYCERATE KINASE, MUTATION R65Q SACCHAROMYCES CEREVISIAE PHOSPHOTRANSFERASE (CARBOXYL ACCEPTOR) KINASE ACETYLATIONGLYCOLYSIS
Ref.: STRUCTURE OF THE R65Q MUTANT OF YEAST 3-PHOSPHOGLYCERATE KINASE COMPLEXED WITH MG-AMP-PNP AND 3-PHOSPHO-D-GLYCERATE. BIOCHEMISTRY V. 35 4118 1996
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1QPG - MAP C10 H16 Mg N6 O12 P3 c1nc(c2c(n....
2 3PGK - 3PG C3 H7 O7 P C([C@H](C(....
70% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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 (32)
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 1VPE - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
31 1PHP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
32 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 DEZ 0.575758 0.941176
3 DER 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 LG6 0.461538 0.941176
10 6PG 0.461538 0.941176
11 HG3 0.451613 0.9375
12 1GP 0.4375 0.852941
13 G3P 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 5SP 0.410256 0.837838
20 D5X 0.410256 0.941176
21 HMS 0.410256 0.837838
22 5RP 0.410256 0.837838
23 0V5 0.40625 0.727273
24 PEQ 0.40625 0.727273
25 RUB 0.4 0.885714
26 XBP 0.4 0.885714
27 RES 0.4 0.659574
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1QPG; Ligand: MAP; Similar sites found with APoc: 82
This union binding pocket(no: 1) in the query (biounit: 1qpg.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5IXB LGA None
2 2IVD FAD 1.20482
3 2IVD ACJ 1.20482
4 5GLN XYP XYP XYP 1.45349
5 1YY5 FAD 1.68675
6 1RSG FAD 1.68675
7 2G50 ALA 1.68675
8 3VOZ 04A 1.90476
9 4JNA FAD 2.05882
10 5JBE MAL 2.16867
11 2GMV PEP 2.16867
12 1PFK ADP 2.1875
13 3LE7 ADE 2.29885
14 4BTV RB3 2.32558
15 5D63 FUC GLA GLA 2.38908
16 4I9B 1KA 2.40964
17 4GKY MAN 2.68199
18 5IDB BMA 2.8169
19 5IDB MAN 2.8169
20 4L80 OXL 2.87356
21 5BWD FUM 2.89157
22 1Q9I FAD 2.89157
23 1Q9I TEO 2.89157
24 3AYI FAD 2.89157
25 3AYI HCI 2.89157
26 4TQK NAG 2.95567
27 4A59 AMP 3.13253
28 1NAA ABL 3.13253
29 1NAA 6FA 3.13253
30 3KJS NAP 3.13253
31 1Z4O GL1 3.16742
32 2W5P CL8 3.3557
33 4P4M D3T 3.43915
34 3GD8 GOL 3.58744
35 1V84 UDP 3.95257
36 1QO8 FAD 4.09639
37 3ITJ CIT 4.14201
38 4WCX ALA 4.33735
39 5XFI NAG NAG BMA MAN MAN NAG GAL NAG 4.57516
40 2X2T GAL NGA 4.57516
41 2D3N GLC GLC GLC 4.57831
42 6F7L FAD 4.57831
43 5LFV SIA GAL NAG 4.73186
44 2GJP MAL 4.81928
45 5H4S RAM 4.92958
46 1GSU GTX 5.02283
47 3HQP FDP 5.06024
48 2IID PHE 5.06024
49 2IID FAD 5.06024
50 3IWK NAD 5.06024
51 3KIH GDL 5.15464
52 5L9O GOP 5.22388
53 3GU3 SAH 5.28169
54 2OL1 UMP 5.44218
55 1H5R G1P 5.46075
56 2HYQ MAN MAN 5.7377
57 2NU5 NAG 5.7377
58 1H16 DTL 5.78313
59 3VPD BUA 6.0241
60 5YB7 FAD 6.0241
61 5YB7 ORN 6.0241
62 2YG3 FAD 6.26506
63 1VBO MAN MAN MAN 6.71141
64 1I1E DM2 6.74699
65 5KQA GSH 6.81818
66 4P6G 2FZ 7.07965
67 2ZX2 RAM 7.17949
68 1V59 NAD 7.46988
69 4Z24 FAD 7.46988
70 1VMK GUN 7.58123
71 3CYQ AMU 7.97101
72 5LQ8 GB 8.15603
73 2VVT DGL 8.27586
74 3KIF GDL 8.49057
75 3R7F CP 8.88158
76 2PYU IMP 9.13242
77 1JG3 ADN 9.78723
78 5YRJ BGC GLC 9.85915
79 3IWD M2T 11.2903
80 3W6X HZP 11.7904
81 2UVO NAG 12.8655
82 1M26 GAL A2G 13.5338
Pocket No.: 2; Query (leader) PDB : 1QPG; Ligand: 3PG; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 1qpg.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 4B98 PXG 1.20482
2 4PIV 2W4 1.68675
3 4EN4 GT1 7.37179
4 4EN4 ATP 7.37179
5 2PYU IMP 9.13242
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