Receptor
PDB id Resolution Class Description Source Keywords
5XA3 2.2 Å EC: 1.14.14.1 CRYSTAL STRUCTURE OF P450BM3 WITH BENZYLOXYCARBONYL-L-PROLYL PHENYLALANINE BACILLUS MEGATERIUM (STRAIN ATCC 14581/ JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / VKM B-5ORGANISM_TAXID: 1348623 CYTOCHROME P450 OXIDOREDUCTASE
Ref.: DIRECT HYDROXYLATION OF BENZENE TO PHENOL BY CYTOCH P450BM3 TRIGGERED BY AMINO ACID DERIVATIVES. ANGEW. CHEM. INT. ED. ENGL. V. 56 10324 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HEM C:501;
A:501;
D:501;
B:501;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
DMS C:502;
A:502;
B:502;
D:502;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
78.133 C2 H6 O S CS(=O...
PRO PHQ PHE D:504;
B:504;
A:504;
C:504;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
395.435 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ZOA 1.74 Å EC: 1.14.14.1 CRYSTAL STRUCTURE OF A328V MUTANT OF THE HEME DOMAIN OF P450 N-PALMITOYLGLYCINE BACILLUS MEGATERIUM CYTOCHROME P-450 HEMEPROTEIN A328V OXIDOREDUCTASE
Ref.: A SINGLE ACTIVE-SITE MUTATION OF P450BM-3 DRAMATICA ENHANCES SUBSTRATE BINDING AND RATE OF PRODUCT FORM BIOCHEMISTRY V. 50 8333 2011
Members (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 6H1L Kd = 24.5 uM FJQ C16 H13 Cl3 N2 O S c1cc(c(cc1....
2 1JPZ Kd = 262 nM 140 C18 H35 N O3 CCCCCCCCCC....
3 6JZS - WAA C31 H40 N2 O3 CC(C)C1=CC....
4 3EKD Kd = 7.4 uM PAM C16 H30 O2 CCCCCCC=C/....
5 6K24 - WAA C31 H40 N2 O3 CC(C)C1=CC....
6 4KEW Kd = 1.67 uM 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
7 4HGG - SYN C8 H8 C=Cc1ccccc....
8 5XA3 - PRO PHQ PHE n/a n/a
9 4DTW Kd = 80 uM SRO C10 H12 N2 O c1cc2c(cc1....
10 6H1O - VOR C16 H14 F3 N5 O C[C@@H](c1....
11 4KEY Kd = 0.212 uM 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
12 4O4P - 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
13 6JS8 - C5R C31 H38 N2 O3 CC(C)c1ccc....
14 4HGH - SYN C8 H8 C=Cc1ccccc....
15 4DTZ Kd = 8.9 uM LDP C8 H11 N O2 c1cc(c(cc1....
16 5DYZ Kd = 0.54 uM 140 C18 H35 N O3 CCCCCCCCCC....
17 4DUB Kd = 1.3 uM LDP C8 H11 N O2 c1cc(c(cc1....
18 3BEN Kd = 0.32 uM LEH C21 H37 N3 O3 CC(C)C[C@@....
19 5JQ2 - 140 C18 H35 N O3 CCCCCCCCCC....
20 6LY4 - TES C19 H28 O2 C[C@]12CC[....
21 4HGI - SYN C8 H8 C=Cc1ccccc....
22 4DUF Kd = 3.3 uM SRO C10 H12 N2 O c1cc2c(cc1....
23 3KX3 - 140 C18 H35 N O3 CCCCCCCCCC....
24 6JLV - WAA C31 H40 N2 O3 CC(C)C1=CC....
25 4KPA Kd = 0.37 uM 140 C18 H35 N O3 CCCCCCCCCC....
26 6H1T Kd = 32.8 uM CL6 C22 H17 Cl N2 c1ccc(cc1)....
27 4HGF - SYN C8 H8 C=Cc1ccccc....
28 6K58 - D0L C21 H32 N2 O3 CCCCCCCN1C....
29 1ZO9 - EPM C21 H41 N O3 S CCCCCCCCCC....
30 4DU2 Kd = 3.3 uM LDP C8 H11 N O2 c1cc(c(cc1....
31 6JVC - WAA C31 H40 N2 O3 CC(C)C1=CC....
32 6JMH - WAA C31 H40 N2 O3 CC(C)C1=CC....
33 6K9S - WAA C31 H40 N2 O3 CC(C)C1=CC....
34 6H1S - TPF C13 H12 F2 N6 O c1cc(c(cc1....
35 4DUE Kd = 0.7 uM SRO C10 H12 N2 O c1cc2c(cc1....
36 6JO1 - BWX C22 H27 N O3 C[C@@H](c1....
37 6JMW - WAA C31 H40 N2 O3 CC(C)C1=CC....
38 1ZOA Kd = 45 nM 140 C18 H35 N O3 CCCCCCCCCC....
70% Homology Family (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6H1L Kd = 24.5 uM FJQ C16 H13 Cl3 N2 O S c1cc(c(cc1....
2 1JPZ Kd = 262 nM 140 C18 H35 N O3 CCCCCCCCCC....
3 6JZS - WAA C31 H40 N2 O3 CC(C)C1=CC....
4 3EKD Kd = 7.4 uM PAM C16 H30 O2 CCCCCCC=C/....
5 6K24 - WAA C31 H40 N2 O3 CC(C)C1=CC....
6 4KEW Kd = 1.67 uM 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
7 4HGG - SYN C8 H8 C=Cc1ccccc....
8 5XA3 - PRO PHQ PHE n/a n/a
9 4DTW Kd = 80 uM SRO C10 H12 N2 O c1cc2c(cc1....
10 6H1O - VOR C16 H14 F3 N5 O C[C@@H](c1....
11 4KEY Kd = 0.212 uM 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
12 4O4P - 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
13 6JS8 - C5R C31 H38 N2 O3 CC(C)c1ccc....
14 4HGH - SYN C8 H8 C=Cc1ccccc....
15 4DTZ Kd = 8.9 uM LDP C8 H11 N O2 c1cc(c(cc1....
16 5DYZ Kd = 0.54 uM 140 C18 H35 N O3 CCCCCCCCCC....
17 4DUB Kd = 1.3 uM LDP C8 H11 N O2 c1cc(c(cc1....
18 3BEN Kd = 0.32 uM LEH C21 H37 N3 O3 CC(C)C[C@@....
19 5JQ2 - 140 C18 H35 N O3 CCCCCCCCCC....
20 6LY4 - TES C19 H28 O2 C[C@]12CC[....
21 4HGI - SYN C8 H8 C=Cc1ccccc....
22 4DUF Kd = 3.3 uM SRO C10 H12 N2 O c1cc2c(cc1....
23 3KX3 - 140 C18 H35 N O3 CCCCCCCCCC....
24 6JLV - WAA C31 H40 N2 O3 CC(C)C1=CC....
25 4KPA Kd = 0.37 uM 140 C18 H35 N O3 CCCCCCCCCC....
26 6H1T Kd = 32.8 uM CL6 C22 H17 Cl N2 c1ccc(cc1)....
27 4HGF - SYN C8 H8 C=Cc1ccccc....
28 6K58 - D0L C21 H32 N2 O3 CCCCCCCN1C....
29 1ZO9 - EPM C21 H41 N O3 S CCCCCCCCCC....
30 4DU2 Kd = 3.3 uM LDP C8 H11 N O2 c1cc(c(cc1....
31 6JVC - WAA C31 H40 N2 O3 CC(C)C1=CC....
32 6JMH - WAA C31 H40 N2 O3 CC(C)C1=CC....
33 6K9S - WAA C31 H40 N2 O3 CC(C)C1=CC....
34 6H1S - TPF C13 H12 F2 N6 O c1cc(c(cc1....
35 4DUE Kd = 0.7 uM SRO C10 H12 N2 O c1cc2c(cc1....
36 6JO1 - BWX C22 H27 N O3 C[C@@H](c1....
37 6JMW - WAA C31 H40 N2 O3 CC(C)C1=CC....
38 1ZOA Kd = 45 nM 140 C18 H35 N O3 CCCCCCCCCC....
50% Homology Family (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6H1L Kd = 24.5 uM FJQ C16 H13 Cl3 N2 O S c1cc(c(cc1....
2 1JPZ Kd = 262 nM 140 C18 H35 N O3 CCCCCCCCCC....
3 6JZS - WAA C31 H40 N2 O3 CC(C)C1=CC....
4 3EKD Kd = 7.4 uM PAM C16 H30 O2 CCCCCCC=C/....
5 6K24 - WAA C31 H40 N2 O3 CC(C)C1=CC....
6 4KEW Kd = 1.67 uM 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
7 4HGG - SYN C8 H8 C=Cc1ccccc....
8 5XA3 - PRO PHQ PHE n/a n/a
9 4DTW Kd = 80 uM SRO C10 H12 N2 O c1cc2c(cc1....
10 6H1O - VOR C16 H14 F3 N5 O C[C@@H](c1....
11 4KEY Kd = 0.212 uM 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
12 4O4P - 1C6 C17 H19 N3 O2 S Cc1cnc(c(c....
13 6JS8 - C5R C31 H38 N2 O3 CC(C)c1ccc....
14 4HGH - SYN C8 H8 C=Cc1ccccc....
15 4DTZ Kd = 8.9 uM LDP C8 H11 N O2 c1cc(c(cc1....
16 5DYZ Kd = 0.54 uM 140 C18 H35 N O3 CCCCCCCCCC....
17 4DUB Kd = 1.3 uM LDP C8 H11 N O2 c1cc(c(cc1....
18 3BEN Kd = 0.32 uM LEH C21 H37 N3 O3 CC(C)C[C@@....
19 5JQ2 - 140 C18 H35 N O3 CCCCCCCCCC....
20 6LY4 - TES C19 H28 O2 C[C@]12CC[....
21 4HGI - SYN C8 H8 C=Cc1ccccc....
22 4DUF Kd = 3.3 uM SRO C10 H12 N2 O c1cc2c(cc1....
23 3KX3 - 140 C18 H35 N O3 CCCCCCCCCC....
24 6JLV - WAA C31 H40 N2 O3 CC(C)C1=CC....
25 4KPA Kd = 0.37 uM 140 C18 H35 N O3 CCCCCCCCCC....
26 6H1T Kd = 32.8 uM CL6 C22 H17 Cl N2 c1ccc(cc1)....
27 4HGF - SYN C8 H8 C=Cc1ccccc....
28 6K58 - D0L C21 H32 N2 O3 CCCCCCCN1C....
29 1ZO9 - EPM C21 H41 N O3 S CCCCCCCCCC....
30 4DU2 Kd = 3.3 uM LDP C8 H11 N O2 c1cc(c(cc1....
31 6JVC - WAA C31 H40 N2 O3 CC(C)C1=CC....
32 6JMH - WAA C31 H40 N2 O3 CC(C)C1=CC....
33 6K9S - WAA C31 H40 N2 O3 CC(C)C1=CC....
34 6H1S - TPF C13 H12 F2 N6 O c1cc(c(cc1....
35 4DUE Kd = 0.7 uM SRO C10 H12 N2 O c1cc2c(cc1....
36 6JO1 - BWX C22 H27 N O3 C[C@@H](c1....
37 6JMW - WAA C31 H40 N2 O3 CC(C)C1=CC....
38 1ZOA Kd = 45 nM 140 C18 H35 N O3 CCCCCCCCCC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PRO PHQ PHE; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 PRO PHQ PHE 1 1
2 TYR MET ASP PHE ASP ASP ASP ILE PRO PHE 0.590361 0.789474
3 HIS PRO PHE 0.573034 0.793103
4 ACE PRO ALA PRO PHE 0.569767 0.762712
5 TRP ASP ILE PRO PHE 0.537634 0.75
6 ALZ 0.52381 0.8
7 THR PRO PRO SER PRO PHE 0.510417 0.730159
8 TYR PRO TYR 0.488372 0.810345
9 ZPR 0.487805 0.814815
10 PKF 0.482456 0.728571
11 DPN PRO ARG 0.453608 0.779661
12 ACE PRO ALA PRO TYR 0.442105 0.714286
13 TYR PRO PHE PHE NH2 0.424242 0.779661
14 MIN 0.414894 0.724138
15 ALA THR PRO PHE GLN GLU 0.412281 0.737705
16 GLY SER ASP PRO PHE LYS 0.405405 0.741935
Similar Ligands (3D)
Ligand no: 1; Ligand: PRO PHQ PHE; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ZOA; Ligand: 140; 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: 1zoa.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1ZOA; Ligand: 140; 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: 1zoa.bio2) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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