Receptor
PDB id Resolution Class Description Source Keywords
4YWD 2.1 Å EC: 4.1.1.32 STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH 2,3-PYRIDIN DICARBOXYLIC ACID RATTUS NORVEGICUS KINASE GLUCONEOGENESIS LYASE
Ref.: INHIBITION AND ALLOSTERIC REGULATION OF MONOMERIC PHOSPHOENOLPYRUVATE CARBOXYKINASE BY 3-MERCAPTOPICO ACID. BIOCHEMISTRY V. 54 5878 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN A:701;
A:702;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
NTM A:704;
Valid;
none;
submit data
167.119 C7 H5 N O4 c1cc(...
NA A:703;
Part of Protein;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1NHX 2.1 Å EC: 4.1.1.32 PEPCK COMPLEX WITH A GTP-COMPETITIVE INHIBITOR HOMO SAPIENS GLUCONEOGENESIS XANTHINE INHIBITOR LYASE
Ref.: X-RAY STRUCTURES OF TWO XANTHINE INHIBITORS BOUND TO PEPCK AND N-3 MODIFICATIONS OF SUBSTITUTED 1,8-DIBENZYLXANTHINES BIOORG.MED.CHEM.LETT. V. 13 3871 2003
Members (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4GMW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4GNO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 5FH1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 4GNL - PEP C3 H5 O6 P C=C(C(=O)O....
5 4GNP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3DT2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 5V9H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 3MOF Ki = 860 uM OXL C2 O4 C(=O)(C(=O....
9 4GNQ - OXL C2 O4 C(=O)(C(=O....
10 2QF2 - OAA C4 H3 O5 C(C(=O)C(=....
11 4GMM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
12 3DT7 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
13 3DTB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5FH3 Ki = 970 uM OXL C2 O4 C(=O)(C(=O....
15 4GMU - OXL C2 O4 C(=O)(C(=O....
16 1KHF - PEP C3 H5 O6 P C=C(C(=O)O....
17 4YW8 - 1WD C6 H5 N O2 S c1cc(c(nc1....
18 4YWD - NTM C7 H5 N O4 c1cc(c(nc1....
19 5FH4 Ki = 174 uM SPV C3 H4 O6 S C(C(=O)C(=....
20 2RKD Ki = 1.9 mM 3PP C3 H7 O5 P C(CP(=O)(O....
21 3MOH Ki = 1460 uM PGA C2 H5 O6 P C(C(=O)O)O....
22 2RK8 Ki = 230 uM PPF C H3 O5 P C(=O)(O)P(....
23 5V9G Ki = 441 uM OXL C2 O4 C(=O)(C(=O....
24 5FH5 - PGA C2 H5 O6 P C(C(=O)O)O....
25 5V9F Ki = 37 uM SPV C3 H4 O6 S C(C(=O)C(=....
26 4YW9 Ki = 45 uM 1WD C6 H5 N O2 S c1cc(c(nc1....
27 3MOE Ki = 50 uM SPV C3 H4 O6 S C(C(=O)C(=....
28 2RK7 Ki = 89 uM OXL C2 O4 C(=O)(C(=O....
29 4GNM - OXL C2 O4 C(=O)(C(=O....
30 2QF1 - OAA C4 H3 O5 C(C(=O)C(=....
31 5FH2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
32 2RKA Ki = 1 mM PGA C2 H5 O6 P C(C(=O)O)O....
33 1M51 ic50 = 18.8 uM TSX C21 H25 N5 O3 CCCCN1c2c(....
34 1NHX ic50 ~ 2.11 uM FTB C25 H26 F N5 O3 CCCCN1c2c(....
35 4GMZ - SPV C3 H4 O6 S C(C(=O)C(=....
36 4OX2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
37 5FH0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
38 5V97 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 1KHB - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
40 3DT4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
41 2RKE Ki = 82.5 uM SAT C2 H4 O5 S C(C(=O)O)S....
42 2QEY - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
43 4YWB - OXD C2 H2 O4 C(=O)(C(=O....
70% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4GMW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4GNO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 5FH1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 4GNL - PEP C3 H5 O6 P C=C(C(=O)O....
5 4GNP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
6 3DT2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 5V9H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
8 3MOF Ki = 860 uM OXL C2 O4 C(=O)(C(=O....
9 4GNQ - OXL C2 O4 C(=O)(C(=O....
10 2QF2 - OAA C4 H3 O5 C(C(=O)C(=....
11 4GMM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
12 3DT7 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
13 3DTB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
14 5FH3 Ki = 970 uM OXL C2 O4 C(=O)(C(=O....
15 4GMU - OXL C2 O4 C(=O)(C(=O....
16 1KHF - PEP C3 H5 O6 P C=C(C(=O)O....
17 4YW8 - 1WD C6 H5 N O2 S c1cc(c(nc1....
18 4YWD - NTM C7 H5 N O4 c1cc(c(nc1....
19 5FH4 Ki = 174 uM SPV C3 H4 O6 S C(C(=O)C(=....
20 2RKD Ki = 1.9 mM 3PP C3 H7 O5 P C(CP(=O)(O....
21 3MOH Ki = 1460 uM PGA C2 H5 O6 P C(C(=O)O)O....
22 2RK8 Ki = 230 uM PPF C H3 O5 P C(=O)(O)P(....
23 5V9G Ki = 441 uM OXL C2 O4 C(=O)(C(=O....
24 5FH5 - PGA C2 H5 O6 P C(C(=O)O)O....
25 5V9F Ki = 37 uM SPV C3 H4 O6 S C(C(=O)C(=....
26 4YW9 Ki = 45 uM 1WD C6 H5 N O2 S c1cc(c(nc1....
27 3MOE Ki = 50 uM SPV C3 H4 O6 S C(C(=O)C(=....
28 2RK7 Ki = 89 uM OXL C2 O4 C(=O)(C(=O....
29 4GNM - OXL C2 O4 C(=O)(C(=O....
30 2QF1 - OAA C4 H3 O5 C(C(=O)C(=....
31 5FH2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
32 2RKA Ki = 1 mM PGA C2 H5 O6 P C(C(=O)O)O....
33 1M51 ic50 = 18.8 uM TSX C21 H25 N5 O3 CCCCN1c2c(....
34 1NHX ic50 ~ 2.11 uM FTB C25 H26 F N5 O3 CCCCN1c2c(....
35 4GMZ - SPV C3 H4 O6 S C(C(=O)C(=....
36 4OX2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
37 5FH0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
38 5V97 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 1KHB - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
40 3DT4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
41 2RKE Ki = 82.5 uM SAT C2 H4 O5 S C(C(=O)O)S....
42 2QEY - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
43 4YWB - OXD C2 H2 O4 C(=O)(C(=O....
44 2GMV ic50 = 0.63 uM UN8 C27 H28 F N7 O4 S CCCCN1c2c(....
45 1KHE - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
46 2QZY - PEP C3 H5 O6 P C=C(C(=O)O....
47 2FAH Ki = 50 mM MLA C3 H4 O4 C(C(=O)O)C....
50% Homology Family (48)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4R43 Kd = 9.3 uM GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
2 4GMW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
3 4GNO - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
4 5FH1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
5 4GNL - PEP C3 H5 O6 P C=C(C(=O)O....
6 4GNP - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
7 3DT2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
8 5V9H - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
9 3MOF Ki = 860 uM OXL C2 O4 C(=O)(C(=O....
10 4GNQ - OXL C2 O4 C(=O)(C(=O....
11 2QF2 - OAA C4 H3 O5 C(C(=O)C(=....
12 4GMM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
13 3DT7 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
14 3DTB - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
15 5FH3 Ki = 970 uM OXL C2 O4 C(=O)(C(=O....
16 4GMU - OXL C2 O4 C(=O)(C(=O....
17 1KHF - PEP C3 H5 O6 P C=C(C(=O)O....
18 4YW8 - 1WD C6 H5 N O2 S c1cc(c(nc1....
19 4YWD - NTM C7 H5 N O4 c1cc(c(nc1....
20 5FH4 Ki = 174 uM SPV C3 H4 O6 S C(C(=O)C(=....
21 2RKD Ki = 1.9 mM 3PP C3 H7 O5 P C(CP(=O)(O....
22 3MOH Ki = 1460 uM PGA C2 H5 O6 P C(C(=O)O)O....
23 2RK8 Ki = 230 uM PPF C H3 O5 P C(=O)(O)P(....
24 5V9G Ki = 441 uM OXL C2 O4 C(=O)(C(=O....
25 5FH5 - PGA C2 H5 O6 P C(C(=O)O)O....
26 5V9F Ki = 37 uM SPV C3 H4 O6 S C(C(=O)C(=....
27 4YW9 Ki = 45 uM 1WD C6 H5 N O2 S c1cc(c(nc1....
28 3MOE Ki = 50 uM SPV C3 H4 O6 S C(C(=O)C(=....
29 2RK7 Ki = 89 uM OXL C2 O4 C(=O)(C(=O....
30 4GNM - OXL C2 O4 C(=O)(C(=O....
31 2QF1 - OAA C4 H3 O5 C(C(=O)C(=....
32 5FH2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
33 2RKA Ki = 1 mM PGA C2 H5 O6 P C(C(=O)O)O....
34 1M51 ic50 = 18.8 uM TSX C21 H25 N5 O3 CCCCN1c2c(....
35 1NHX ic50 ~ 2.11 uM FTB C25 H26 F N5 O3 CCCCN1c2c(....
36 4GMZ - SPV C3 H4 O6 S C(C(=O)C(=....
37 4OX2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
38 5FH0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
39 5V97 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
40 1KHB - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
41 3DT4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
42 2RKE Ki = 82.5 uM SAT C2 H4 O5 S C(C(=O)O)S....
43 2QEY - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
44 4YWB - OXD C2 H2 O4 C(=O)(C(=O....
45 2GMV ic50 = 0.63 uM UN8 C27 H28 F N7 O4 S CCCCN1c2c(....
46 1KHE - GCP C11 H18 N5 O13 P3 c1nc2c(n1[....
47 2QZY - PEP C3 H5 O6 P C=C(C(=O)O....
48 2FAH Ki = 50 mM MLA C3 H4 O4 C(C(=O)O)C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NTM; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 NTM 1 1
2 1WD 0.513514 0.666667
3 3GQ 0.4 0.666667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1NHX; Ligand: FTB; 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: 1nhx.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1NHX; Ligand: PEP; 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: 1nhx.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
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