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Receptor
PDB id Resolution Class Description Source Keywords
2XD9 1.95 Å EC: 4.2.1.10 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN C WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-TRIHYDROXY-2-((E)-E NYL)-4,5,6,7-TETRAHYDROBENZO(B)THIOPHENE-4-CARBOXYLIC ACID HELICOBACTER PYLORI AROMATIC AMINO ACID BIOSYNTHESIS LYASE
Ref.: TETRAHYDROBENZOTHIOPHENE DERIVATIVES: CONFORMATIONA RESTRICTED INHIBITORS OF TYPE II DEHYDROQUINASE. CHEMMEDCHEM V. 6 266 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
XD9 A:200;
B:200;
C:200;
Valid;
Valid;
Valid;
none;
none;
none;
Ki = 0.35 uM
270.302 C12 H14 O5 S CC=Cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2XD9 1.95 Å EC: 4.2.1.10 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN C WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-TRIHYDROXY-2-((E)-E NYL)-4,5,6,7-TETRAHYDROBENZO(B)THIOPHENE-4-CARBOXYLIC ACID HELICOBACTER PYLORI AROMATIC AMINO ACID BIOSYNTHESIS LYASE
Ref.: TETRAHYDROBENZOTHIOPHENE DERIVATIVES: CONFORMATIONA RESTRICTED INHIBITORS OF TYPE II DEHYDROQUINASE. CHEMMEDCHEM V. 6 266 2011
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 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 9ZT C15 H18 O7 COc1ccc(cc....
5 4B6S Ki = 970 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
70% Homology Family (5)
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 9ZT C15 H18 O7 COc1ccc(cc....
5 4B6S Ki = 970 nM 2HN C14 H11 F5 O6 C1[C@H]([C....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 9ZT 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
Ligand no: 1; Ligand: XD9; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 XD9 1 1
2 JPS 0.471429 0.85
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2XD9; Ligand: XD9; Similar sites found with APoc: 13
This union binding pocket(no: 1) in the query (biounit: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
1 3GON PMV 1.1976
2 6CI9 F3V 2.99401
3 3UG4 AHR 3.59281
4 4EKQ NPO 4.19162
5 5GQX GLC GLC GLC 4.79042
6 2QX0 PH2 5.03145
7 3GUZ PAF 6.58683
8 4ZUL UN1 6.82261
9 5E70 RCD 11.976
10 1OFZ FUC 14.3713
11 1OFZ FUL 14.3713
12 4LIK CIT 17.9641
13 3NJQ NJQ 20.9581
Pocket No.: 2; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2XD9; Ligand: XD9; Similar sites found with APoc: 17
This union binding pocket(no: 5) in the query (biounit: 2xd9.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 1TUK PGM None
2 4FBL SPD 3.91459
3 2IMP LAC 4.19162
4 5E58 CPZ 4.19162
5 5EHS 5OY 4.79042
6 5EHS 2JJ 4.79042
7 1VJ7 GPX 5.98802
8 2H6B 3C4 5.98802
9 3KIH GDL 6.18557
10 1DTL BEP 6.21118
11 4GNC ASO 7.18563
12 4GQY AMP 8.48485
13 1TE2 PGA 8.98204
14 2AJH MET 9.58084
15 4V3I ASP LEU THR ARG PRO 10.8949
16 3V0H I3P 13.1737
17 2BS5 BGC GAL FUC 20
Pocket No.: 6; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 2XD9; Ligand: XD9; 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: 2xd9.bio1) has 59 residues
No: Leader PDB Ligand Sequence Similarity
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