Receptor
PDB id Resolution Class Description Source Keywords
3DU4 2.2 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7-KETO-8-AMINOPELARGONIC ACID BOUND 7,8 DIAMINOPELARGONIC ACID SYNTHASE IN BACILLUS SUBTILIS BACILLUS SUBTILIS AMINOTRANSFERASE BIOTIN BIOSYNTHESIS PYRIDOXAL PHOSPHATE ADENOSYL-L-METHIONINE 7-KETO 8-AMINO PELARGONIC ACID TRA
Ref.: STRUCTURAL CHARACTERIZATION OF THE MYCOBACTERIUM TUBERCULOSIS BIOTIN BIOSYNTHESIS ENZYMES 7,8-DIAMINOPELARGONIC ACID SYNTHASE AND DETHIOBIOTI SYNTHETASE . BIOCHEMISTRY V. 49 6746 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KAP A:451;
B:451;
Valid;
Valid;
none;
none;
submit data
187.236 C9 H17 N O3 C[C@@...
PLP A:450;
B:450;
Part of Protein;
Part of Protein;
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
3DU4 2.2 Å EC: 2.6.1.62 CRYSTAL STRUCTURE OF 7-KETO-8-AMINOPELARGONIC ACID BOUND 7,8 DIAMINOPELARGONIC ACID SYNTHASE IN BACILLUS SUBTILIS BACILLUS SUBTILIS AMINOTRANSFERASE BIOTIN BIOSYNTHESIS PYRIDOXAL PHOSPHATE ADENOSYL-L-METHIONINE 7-KETO 8-AMINO PELARGONIC ACID TRA
Ref.: STRUCTURAL CHARACTERIZATION OF THE MYCOBACTERIUM TUBERCULOSIS BIOTIN BIOSYNTHESIS ENZYMES 7,8-DIAMINOPELARGONIC ACID SYNTHASE AND DETHIOBIOTI SYNTHETASE . BIOCHEMISTRY V. 49 6746 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3DU4 - KAP C9 H17 N O3 C[C@@H](C(....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3DU4 - KAP C9 H17 N O3 C[C@@H](C(....
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WYC Kd = 15 uM 3VS C10 H9 N3 O c1cc(ccc1C....
2 4CXR - 2BG C8 H8 N2 S c1ccc2c(c1....
3 3TFU - PL8 C16 H22 N3 O7 P Cc1c(c(c(c....
4 4MQR - 2B9 C14 H15 N4 O6 P CC1=C(/C(=....
5 4MQP - 2B1 C15 H15 N4 O5 P S Cc1c(c(c(c....
6 4XJO Kd = 132 nM 41O C20 H17 Cl N2 O2 c1cc(cc(c1....
7 5KGS Kd = 74 nM 6SR C21 H20 N2 O4 c1cc2c(cc1....
8 4W1W ic50 = 0.195 uM 3G8 C18 H17 N O3 S CCN(CC)c1c....
9 4WYG Kd = 6.8 uM 3W1 C11 H12 Cl N3 c1cc(ccc1C....
10 4MQQ - 2B6 C16 H15 N4 O6 P S Cc1c(c(c(c....
11 4XEW ic50 = 0.44 uM 40N C16 H10 F N O3 c1ccc(c(c1....
12 4W1V ic50 = 0.659 uM 3GS C16 H14 F N O5 S COC(=O)c1c....
13 4XJP Kd = 108 nM 41N C20 H20 N2 O4 CC(=O)c1cc....
14 4WYF Kd = 21.7 uM 3VX C11 H9 N O2 CC(=O)Nc1c....
15 4WYA Kd = 6.9 uM 3VQ C10 H8 N2 O S c1ccnc(c1)....
16 4W1X - 3G9 C19 H19 Cl N2 O2 CC(=O)c1cc....
17 5KGT - 6SQ C20 H20 Cl N O2 CC(=O)c1cc....
18 4WYE Kd = 41.8 uM 3VW C12 H15 N O c1ccc(cc1)....
19 4CXQ - KAP C9 H17 N O3 C[C@@H](C(....
20 4WYD Kd = 11.7 uM 3VR C12 H15 N3 CNCc1ccc(c....
21 3LV2 - SFG C15 H23 N7 O5 c1nc(c2c(n....
22 5TE2 - 7B9 C16 H22 N3 O7 P Cc1c(c(c(c....
23 4B9B - PLP C8 H10 N O6 P Cc1c(c(c(c....
24 4B98 - PXG C15 H17 N2 O7 P Cc1c(c(c(c....
25 1MLZ - TZA PLP n/a n/a
26 1MLY - ACZ PLP n/a n/a
27 1S07 - PLP C8 H10 N O6 P Cc1c(c(c(c....
28 3DU4 - KAP C9 H17 N O3 C[C@@H](C(....
29 3A8U - PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KAP; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 KAP 1 1
2 PML 0.551724 0.62069
3 DNN 0.5 0.75
4 AZ1 0.483871 0.6
5 SHV 0.470588 0.6
6 ACA 0.457143 0.625
7 IKT 0.454545 0.896552
8 011 0.444444 0.606061
9 DSD 0.444444 0.666667
10 NPI 0.435897 0.741935
11 8AC 0.432432 0.606061
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DU4; Ligand: KAP; Similar sites found: 7
This union binding pocket(no: 1) in the query (biounit: 3du4.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4AQ4 G3P 0.01081 0.40337 1.90931
2 2WL9 MBD 0.005257 0.42189 2.29508
3 3NYQ MCA 0.04883 0.40141 2.67857
4 5EYK 5U5 0.03361 0.40431 9.05797
5 2YKX AKG 0.002554 0.43249 26.3393
6 3FQ8 PMP 0.02709 0.40514 30.9133
7 5G09 6DF 0.000473 0.49045 41.0714
Pocket No.: 2; Query (leader) PDB : 3DU4; Ligand: KAP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3du4.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback