Receptor
PDB id Resolution Class Description Source Keywords
6C4A 1.8 Å EC: 4.1.3.1 CRYSTAL STRUCTURE OF 3-NITROPROPIONATE MODIFIED ISOCITRATE L MYCOBACTERIUM TUBERCULOSIS WITH PYRUVATE MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCTMC 107 / ERDMAN) LYASE
Ref.: THE NITRO GROUP AS A MASKED ELECTROPHILE IN COVALEN INHIBITION. ACS CHEM. BIOL. V. 13 1470 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3NP C:505;
B:502;
Invalid;
Invalid;
none;
none;
submit data
119.076 C3 H5 N O4 C(C[N...
MG F:505;
H:503;
B:501;
D:502;
G:504;
D:503;
H:504;
C:502;
G:506;
A:502;
H:501;
A:503;
F:503;
B:505;
E:502;
G:502;
B:504;
F:504;
C:503;
H:505;
E:503;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Invalid;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
PYR G:501;
B:503;
H:502;
D:501;
E:501;
C:501;
F:502;
A:501;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
88.062 C3 H4 O3 CC(=O...
EPE F:501;
G:503;
Invalid;
Invalid;
none;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
PEG G:505;
H:506;
C:504;
E:504;
F:506;
D:504;
B:506;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
106.12 C4 H10 O3 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6C4A 1.8 Å EC: 4.1.3.1 CRYSTAL STRUCTURE OF 3-NITROPROPIONATE MODIFIED ISOCITRATE L MYCOBACTERIUM TUBERCULOSIS WITH PYRUVATE MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCTMC 107 / ERDMAN) LYASE
Ref.: THE NITRO GROUP AS A MASKED ELECTROPHILE IN COVALEN INHIBITION. ACS CHEM. BIOL. V. 13 1470 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6C4A - PYR C3 H4 O3 CC(=O)C(=O....
2 1F8I - SIN C4 H6 O4 C(CC(=O)O)....
3 6C4C - PYR C3 H4 O3 CC(=O)C(=O....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6C4A - PYR C3 H4 O3 CC(=O)C(=O....
2 1F8I - SIN C4 H6 O4 C(CC(=O)O)....
3 6C4C - PYR C3 H4 O3 CC(=O)C(=O....
4 1IGW - PYR C3 H4 O3 CC(=O)C(=O....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6C4A - PYR C3 H4 O3 CC(=O)C(=O....
2 1F8I - SIN C4 H6 O4 C(CC(=O)O)....
3 6C4C - PYR C3 H4 O3 CC(=O)C(=O....
4 1IGW - PYR C3 H4 O3 CC(=O)C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PYR; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 PYR 1 1
2 ACY 0.636364 0.636364
3 OXD 0.545455 0.642857
4 F50 0.428571 0.6
5 2KT 0.411765 0.733333
6 AAE 0.411765 0.625
7 KIV 0.411765 0.785714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6C4A; Ligand: PYR; 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: 6c4a.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6C4A; Ligand: PYR; 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: 6c4a.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6C4A; Ligand: PYR; 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: 6c4a.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6C4A; Ligand: PYR; 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: 6c4a.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6C4A; Ligand: PYR; 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: 6c4a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6C4A; Ligand: PYR; 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: 6c4a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 6C4A; Ligand: PYR; 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: 6c4a.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 6C4A; Ligand: PYR; 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: 6c4a.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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