Receptor
PDB id Resolution Class Description Source Keywords
4ciy 2.1 Å EC: 4.2.1.10 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE 2 DEHYD IN COMPLEX WITH (1R,4R,5R)-1,4,5-TRIHYDROXY-3-((1R)-1-HYDROP HENYL)ETHYLCYCLOHEX-2-EN-1-CARBOXYLIC ACID MYCOBACTERIUM TUBERCULOSIS LYASE INHIBITOR PROTEIN BINDING SHIKIMIS ACID P SUBSTRATESPECIFICITY
Ref.: EXPLORING THE WATER-BINDING POCKET OF THE TYPE II DEHYDROQUINASE ENZYME IN THE STRUCTURE-BASED DESIGN INHIBITORS. J. MED. CHEM. V. 57 3494 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA A:1148;
A:1149;
A:1147;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
CL A:1146;
Invalid;
none;
submit data
35.453 Cl [Cl-]
NDY A:1144;
Valid;
none;
Ki = 27 uM
294.3 C15 H18 O6 c1ccc...
SO4 A:1145;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2XB8 2.4 Å EC: 4.2.1.10 STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TYPE II DEHYDROQUINA COMPLEX WITH INHIBITOR COMPOUND (2R)-2-(4-METHOXYBENZYL)-3-D EHYDROQUINIC ACID MYCOBACTERIUM TUBERCULOSIS LYASE AMINO ACID BIOSYNTHESIS
Ref.: UNDERSTANDING THE KEY FACTORS THAT CONTROL THE INHI TYPE II DEHYDROQUINASE BY (2R)-2- BENZYL-3-DEHYDROQ ACIDS. CHEMMEDCHEM V. 5 1726 2010
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3N87 Ki = 11 uM N87 C20 H18 O6 c1ccc(cc1)....
2 2Y76 Ki = 440 nM CB7 C25 H22 O6 S2 c1cc2c(ccs....
3 3N7A Ki = 200 uM FA1 C7 H10 O5 C1[C@H]([C....
4 4B6O Ki = 100 nM 3DQ C15 H18 O7 COc1ccc(cc....
5 2Y71 Ki = 42.5 nM CB6 C17 H18 O6 S Cc1ccc2c(c....
6 4CIW Ki = 15 uM XH2 C9 H14 O6 C1[C@H]([C....
7 4B6P Ki = 74 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
8 3N8N Ki = 27 uM N88 C12 H19 N O6 CC(C)(C)NC....
9 3N76 Ki = 0.14 uM CA2 C16 H22 O6 c1ccc(cc1)....
10 4CIY Ki = 27 uM NDY C15 H18 O6 c1ccc(cc1)....
11 1H0R Ki = 200 uM FA1 C7 H10 O5 C1[C@H]([C....
12 3N86 Ki = 2.3 uM RJP C16 H17 N O6 c1ccc(cc1)....
13 2XB8 Ki = 26 nM XNW C15 H18 O7 COc1ccc(cc....
14 1H0S - FA6 C7 H11 N O6 C1[C@H]([C....
15 4B6Q Ki = 28 nM BZ5 C16 H16 O6 S c1cc2c(ccs....
16 2Y77 Ki = 250 nM CB8 C21 H20 O6 S2 c1ccc2c(c1....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3N87 Ki = 11 uM N87 C20 H18 O6 c1ccc(cc1)....
2 2Y76 Ki = 440 nM CB7 C25 H22 O6 S2 c1cc2c(ccs....
3 3N7A Ki = 200 uM FA1 C7 H10 O5 C1[C@H]([C....
4 4B6O Ki = 100 nM 3DQ C15 H18 O7 COc1ccc(cc....
5 2Y71 Ki = 42.5 nM CB6 C17 H18 O6 S Cc1ccc2c(c....
6 4CIW Ki = 15 uM XH2 C9 H14 O6 C1[C@H]([C....
7 4B6P Ki = 74 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
8 3N8N Ki = 27 uM N88 C12 H19 N O6 CC(C)(C)NC....
9 3N76 Ki = 0.14 uM CA2 C16 H22 O6 c1ccc(cc1)....
10 4CIY Ki = 27 uM NDY C15 H18 O6 c1ccc(cc1)....
11 1H0R Ki = 200 uM FA1 C7 H10 O5 C1[C@H]([C....
12 3N86 Ki = 2.3 uM RJP C16 H17 N O6 c1ccc(cc1)....
13 2XB8 Ki = 26 nM XNW C15 H18 O7 COc1ccc(cc....
14 1H0S - FA6 C7 H11 N O6 C1[C@H]([C....
15 4B6Q Ki = 28 nM BZ5 C16 H16 O6 S c1cc2c(ccs....
16 2Y77 Ki = 250 nM CB8 C21 H20 O6 S2 c1ccc2c(c1....
17 3N8K Kd = 90 uM D1X C6 H5 N O4 C1C(=CC(=O....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2XDA Ki = 0.6 uM JPS C14 H18 O5 S c1c(sc2c1[....
2 2XD9 Ki = 0.35 uM XD9 C12 H14 O5 S CC=Cc1cc2c....
3 2C4W Ki = 20 uM GAJ C14 H9 N5 O4 S c1ccc2c(c1....
4 4B6R Ki = 1420 nM 3DQ C15 H18 O7 COc1ccc(cc....
5 4B6S Ki = 970 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
6 3N76 Ki = 0.14 uM CA2 C16 H22 O6 c1ccc(cc1)....
7 4CIY Ki = 27 uM NDY C15 H18 O6 c1ccc(cc1)....
8 1H0R Ki = 200 uM FA1 C7 H10 O5 C1[C@H]([C....
9 3N86 Ki = 2.3 uM RJP C16 H17 N O6 c1ccc(cc1)....
10 2XB8 Ki = 26 nM XNW C15 H18 O7 COc1ccc(cc....
11 1H0S - FA6 C7 H11 N O6 C1[C@H]([C....
12 4B6Q Ki = 28 nM BZ5 C16 H16 O6 S c1cc2c(ccs....
13 2Y77 Ki = 250 nM CB8 C21 H20 O6 S2 c1ccc2c(c1....
14 2BT4 Ki = 33 uM CA2 C16 H22 O6 c1ccc(cc1)....
15 1V1J Ki = 15 uM FA3 C7 H9 F O5 C1[C@H]([C....
16 2CJF Ki = 380 nM RP4 C19 H18 O5 S c1ccc(cc1)....
17 1GU1 Ki = 30 uM FA1 C7 H10 O5 C1[C@H]([C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NDY; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NDY 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: NDY; Similar ligands found: 8
No: Ligand Similarity coefficient
1 CMG 0.8834
2 NU3 0.8783
3 5PK 0.8769
4 GAT 0.8685
5 3DQ 0.8669
6 4K2 0.8656
7 JPS 0.8631
8 N88 0.8524
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2XB8; Ligand: XNW; 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: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2XB8; Ligand: XNW; 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: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 2XB8; Ligand: XNW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 2xb8.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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