Receptor
PDB id Resolution Class Description Source Keywords
5iw8 2.04 Å EC: 2.5.1.113 MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCA INHIBITOR 4 [5-(3-([1,1'-BIPHENYL]-3-YL)UREIDO)-2-HYDROXYBEA CID] MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) MYCOBACTERIUM TUBERCULOSIS CYSTEINE BIOSYNTHESIS SULPHUR METABOLISM INHIBITOR LYASE
Ref.: INHIBITORS OF THE CYSTEINE SYNTHASE CYSM WITH ANTIB POTENCY AGAINST DORMANT MYCOBACTERIUM TUBERCULOSIS. J.MED.CHEM. V. 59 6848 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6EC A:401;
B:401;
 Valid;
Valid;
 none;
none;
 Kd = 2.2 uM
348.352 C20 H16 N2 O4 c1ccc...
NA A:402;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
PLP B:402;
A:403;
 Invalid;
Invalid;
 none;
none;
 submit data
247.142 C8 H10 N O6 P Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5I7A 2.08 Å EC: 2.5.1.113 MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCA INHIBITOR 1 [3-(3-(3,4-DICHLOROPHENYL)UREIDO)BENZOIC ACID] MYCOBACTERIUM TUBERCULOSIS MYCOBACTERIUM TUBERCULOSIS CYSTEINE BIOSYNTHESIS SULPHUR METABOLISM INHIBITOR TRANSFERASE LYASE
Ref.: INHIBITORS OF THE CYSTEINE SYNTHASE CYSM WITH ANTIB POTENCY AGAINST DORMANT MYCOBACTERIUM TUBERCULOSIS. J.MED.CHEM. V. 59 6848 2016
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5I7A Kd = 0.32 uM 68Q C14 H10 Cl2 N2 O3 c1cc(cc(c1....
2 5I7R Kd = 1.7 uM 68W C20 H16 N2 O3 c1ccc(cc1)....
3 5I7O Kd = 3.4 uM S16 C14 H11 Cl N2 O3 c1cc(cc(c1....
4 5I6D Kd = 8 uM AU6 C15 H14 N2 O3 Cc1ccc(cc1....
5 5IW8 Kd = 2.2 uM 6EC C20 H16 N2 O4 c1ccc(cc1)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5I7A Kd = 0.32 uM 68Q C14 H10 Cl2 N2 O3 c1cc(cc(c1....
2 5I7R Kd = 1.7 uM 68W C20 H16 N2 O3 c1ccc(cc1)....
3 5I7O Kd = 3.4 uM S16 C14 H11 Cl N2 O3 c1cc(cc(c1....
4 5I6D Kd = 8 uM AU6 C15 H14 N2 O3 Cc1ccc(cc1....
5 5IW8 Kd = 2.2 uM 6EC C20 H16 N2 O4 c1ccc(cc1)....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1Y7L Ki = 130 nM GLY ILE ASP ASP GLY MET ASN LEU ASN ILE n/a n/a
2 3IQG Kd = 24.9 uM MET ASN TRP ASN ILE n/a n/a
3 3IQH Kd = 25.8 uM MET ASN TYR ASP ILE n/a n/a
4 3IQI Kd = 38.7 uM MET ASN GLU ASN ILE n/a n/a
5 4LMB Kd = 186 uM CYS CYS n/a n/a
6 5I7A Kd = 0.32 uM 68Q C14 H10 Cl2 N2 O3 c1cc(cc(c1....
7 5I7R Kd = 1.7 uM 68W C20 H16 N2 O3 c1ccc(cc1)....
8 5I7O Kd = 3.4 uM S16 C14 H11 Cl N2 O3 c1cc(cc(c1....
9 5I6D Kd = 8 uM AU6 C15 H14 N2 O3 Cc1ccc(cc1....
10 5IW8 Kd = 2.2 uM 6EC C20 H16 N2 O4 c1ccc(cc1)....
11 3X44 - PUS C12 H17 N4 O9 P Cc1c(c(c(c....
12 2Q3D - PDA C11 H17 N2 O7 P Cc1c(c(c(c....
13 2Q3C Ki = 5 uM ASP PHE SER ILE n/a n/a
14 3ZEI ic50 = 0.103 uM AWH C20 H16 N2 O6 S CN1C(=O)/C....
15 4IL5 - ILE C6 H13 N O2 CC[C@H](C)....
16 4JBN - SER PRO SER ILE n/a n/a
17 4JBL Kd = 0.54 mM MET C5 H11 N O2 S CSCC[C@@H]....
18 3BM5 Kd = 1.1 mM CYS C3 H7 N O2 S C([C@@H](C....
19 1D6S Kd = 78 uM MET PLP n/a n/a
20 3VC3 - C6P C11 H17 N2 O7 P S Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 6EC; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 6EC 1 1
2 68W 0.619048 0.820513
Similar Ligands (3D)
Ligand no: 1; Ligand: 6EC; Similar ligands found: 12
No: Ligand Similarity coefficient
1 6M8 0.8986
2 4F7 0.8981
3 0J6 0.8885
4 5WD 0.8860
5 LI3 0.8841
6 D6X 0.8794
7 0J7 0.8775
8 NXP 0.8728
9 5M9 0.8720
10 38O 0.8705
11 M7K 0.8680
12 4GK 0.8625
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5I7A; Ligand: 68Q; 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: 5i7a.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5I7A; Ligand: 68Q; 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: 5i7a.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5I7A; Ligand: 68Q; 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: 5i7a.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5I7A; Ligand: 68Q; 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: 5i7a.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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