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Receptor
PDB id Resolution Class Description Source Keywords
2P9T 2 Å EC: 2.7.2.3 CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE-2 BOUND TO 3- PHOSPHOGLYCERATE MUS MUSCULUS TRANSFERASE PHOSPHOGLYCERATE KINSE ENZYME-SUBSTRATE COMPLE
Ref.: X-RAY ANALYSIS OF PHOSPHOGLYCERATE KINASE 2, A SPERM-SPECIFIC ISOFORM FROM MUS MUSCULUS. PROTEINS V. 71 1134 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PG A:500;
Valid;
none;
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186.057 C3 H7 O7 P C([C@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2P9T 2 Å EC: 2.7.2.3 CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE KINASE-2 BOUND TO 3- PHOSPHOGLYCERATE MUS MUSCULUS TRANSFERASE PHOSPHOGLYCERATE KINSE ENZYME-SUBSTRATE COMPLE
Ref.: X-RAY ANALYSIS OF PHOSPHOGLYCERATE KINASE 2, A SPERM-SPECIFIC ISOFORM FROM MUS MUSCULUS. PROTEINS V. 71 1134 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2P9T - 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 : 2P9T; Ligand: 3PG; Similar sites found with APoc: 34
This union binding pocket(no: 1) in the query (biounit: 2p9t.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 2PTM CMP 1.0101
2 1ZXM ANP 1.5
3 4IDT T28 1.68539
4 1XPM CAA 1.76768
5 1XPK HMG 1.80412
6 5U5G NAP 2.0339
7 2Q2Y MKR 2.17984
8 2Q2Y ADP 2.17984
9 6C8R EQV 2.37467
10 1NAA ABL 2.40385
11 1NAA 6FA 2.40385
12 3T7S SAM 2.61194
13 4RJK TPP 2.8021
14 2WL5 COA 2.80612
15 2G5C NAD 2.84698
16 1M2K APR 3.21285
17 3B8I OXL 3.48432
18 1EE0 CAA 3.9801
19 3WQQ NDP 4.32692
20 3WQQ IB3 4.32692
21 2PHF MAN MAN BMA MAN 4.36508
22 2PHR MAN MAN BMA MAN 4.36508
23 5BNW 12V 4.56731
24 3CK8 BCD 4.56731
25 4GYW UDP 4.56731
26 3A5Z KAA 5.2356
27 5DM1 5D7 5.99251
28 5DM1 SAH 5.99251
29 2E5A LAQ 6.05187
30 2D0V PQQ 6.49038
31 5TVF CGQ 6.66667
32 1H65 GDP 11.4815
33 3AHQ FAD 12.9808
34 4RPO T6C 17.9372
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