Receptor
PDB id Resolution Class Description Source Keywords
2VBB 1.4 Å EC: 1.21.3.1 ISOPENICILLIN N SYNTHASE WITH SUBSTRATE ANALOGUE ACOMP ( 35MINUTES OXYGEN EXPOSURE) EMERICELLA NIDULANS OXIDOREDUCTASE ANTIBIOTIC BIOSYNTHESIS PENICILLIN BIOSYNTHIRON OXYGENASE VITAMIN C METAL-BINDING MONOCYCLIC INTERB-LACTAM ANTIBIOTIC
Ref.: ISOPENICILLIN N SYNTHASE MEDIATES THIOLATE OXIDATIO SULFENATE IN A DEPSIPEPTIDE SUBSTRATE ANALOGUE: IMPLICATIONS FOR OXYGEN BINDING AND A LINK TO NITRI HYDRATASE? J.AM.CHEM.SOC. V. 130 10096 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE2 A:1333;
Part of Protein;
none;
submit data
55.845 Fe [Fe+2...
GOL A:1336;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:1334;
A:1335;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
VAZ A:1332;
Valid;
none;
submit data
414.452 C13 H22 N2 O9 S2 CS[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ODM 1.15 Å EC: 1.21.3.1 ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (ANAEROBI VINYLGLYCINE FE COMPLEX) EMERICELLA NIDULANS ANTIBIOTIC BIOSYNTHESIS B-LACTAM ANTIBIOTIC OXYGENASE PENBIOSYNTHESIS OXIDOREDUCTASE IRON
Ref.: CRYSTALLOGRAPHIC STUDIES ON THE REACTION OF ISOPENI SYNTHASE WITH AN UNSATURATED SUBSTRATE ANALOGUE ORG.BIOMOL.CHEM. V. 1 1455 2003
Members (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3ZKY - WT4 C14 H25 N3 O6 S2 CSC[C@H](C....
2 2Y6F - M9F C14 H25 N3 O6 S2 CC([C@H](C....
3 1HB2 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
4 1ODN - APV C13 H19 N3 O7 S C(C[C@@H](....
5 2VBB - VAZ C13 H22 N2 O9 S2 CS[C@@H]([....
6 3ZKU - HCV C15 H27 N3 O6 S CC(C)[C@H]....
7 2VBP - VB1 C13 H23 N3 O6 S CC[C@@H](C....
8 4BB3 - KKA C10 H18 N2 O5 S C(C[C@@H](....
9 1QJE - IP1 C14 H21 N3 O6 S CC1([C@@H]....
10 1HB4 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
11 2BU9 - HFV C14 H19 F6 N3 O6 S C(C[C@@H](....
12 1W06 - W05 C12 H21 N3 O6 S C[C@H](C(=....
13 1OC1 - ASV C13 H21 N3 O6 S C=C[C@H](C....
14 1HB1 - OCV C14 H24 N2 O7 S CC(C)[C@H]....
15 2IVJ - BCV C14 H23 N3 O6 S C1CC1[C@H]....
16 2JB4 - A14 C15 H22 N2 O6 S CC1([C@@H]....
17 2VCM - M11 C15 H26 N2 O7 S CC(C)[C@H]....
18 1W04 - HCG C11 H19 N3 O6 S C(C[C@@H](....
19 1W3X - W2X C15 H24 N2 O8 S C[C@H](CO)....
20 6Y0O - ACV C14 H25 N3 O6 S CC(C)[C@H]....
21 1HB3 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
22 1ODM - ASV C13 H21 N3 O6 S C=C[C@H](C....
23 2Y60 - M8F C14 H25 N3 O6 S2 CSCC[C@H](....
24 1W3V - MDZ C15 H26 N2 O7 S CC(C)[C@H]....
25 1QJF - ACS C13 H21 N3 O7 S2 C[S@](=O)C....
26 1UZW - CDH C14 H23 N3 O6 S CC(=C)[C@H....
27 2IVI - ACW C15 H25 N3 O6 S CC1(CC1)[C....
28 2VAU - V20 C13 H22 N2 O7 S2 CSC[C@H](C....
29 1W03 - HCG C11 H19 N3 O6 S C(C[C@@H](....
30 1BK0 - ACV C14 H25 N3 O6 S CC(C)[C@H]....
31 1OBN - ASV C13 H21 N3 O6 S C=C[C@H](C....
32 3ZOI - M2W C14 H25 N3 O7 S C[C@@H]([C....
33 2VBD - V10 C13 H22 N2 O7 S2 CSC[C@@H](....
34 1W05 - W05 C12 H21 N3 O6 S C[C@H](C(=....
35 2WO7 - ASV C13 H21 N3 O6 S C=C[C@H](C....
36 1QIQ - ACC C13 H24 N3 O6 S2 CSC[C@H](C....
37 1BLZ - ACV C14 H25 N3 O6 S CC(C)[C@H]....
70% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3ZKY - WT4 C14 H25 N3 O6 S2 CSC[C@H](C....
2 2Y6F - M9F C14 H25 N3 O6 S2 CC([C@H](C....
3 1HB2 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
4 1ODN - APV C13 H19 N3 O7 S C(C[C@@H](....
5 2VBB - VAZ C13 H22 N2 O9 S2 CS[C@@H]([....
6 3ZKU - HCV C15 H27 N3 O6 S CC(C)[C@H]....
7 2VBP - VB1 C13 H23 N3 O6 S CC[C@@H](C....
8 4BB3 - KKA C10 H18 N2 O5 S C(C[C@@H](....
9 1QJE - IP1 C14 H21 N3 O6 S CC1([C@@H]....
10 1HB4 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
11 2BU9 - HFV C14 H19 F6 N3 O6 S C(C[C@@H](....
12 1W06 - W05 C12 H21 N3 O6 S C[C@H](C(=....
13 1OC1 - ASV C13 H21 N3 O6 S C=C[C@H](C....
14 1HB1 - OCV C14 H24 N2 O7 S CC(C)[C@H]....
15 2IVJ - BCV C14 H23 N3 O6 S C1CC1[C@H]....
16 2JB4 - A14 C15 H22 N2 O6 S CC1([C@@H]....
17 2VCM - M11 C15 H26 N2 O7 S CC(C)[C@H]....
18 1W04 - HCG C11 H19 N3 O6 S C(C[C@@H](....
19 1W3X - W2X C15 H24 N2 O8 S C[C@H](CO)....
20 6Y0O - ACV C14 H25 N3 O6 S CC(C)[C@H]....
21 1HB3 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
22 1ODM - ASV C13 H21 N3 O6 S C=C[C@H](C....
23 2Y60 - M8F C14 H25 N3 O6 S2 CSCC[C@H](....
24 1W3V - MDZ C15 H26 N2 O7 S CC(C)[C@H]....
25 1QJF - ACS C13 H21 N3 O7 S2 C[S@](=O)C....
26 1UZW - CDH C14 H23 N3 O6 S CC(=C)[C@H....
27 2IVI - ACW C15 H25 N3 O6 S CC1(CC1)[C....
28 2VAU - V20 C13 H22 N2 O7 S2 CSC[C@H](C....
29 1W03 - HCG C11 H19 N3 O6 S C(C[C@@H](....
30 1BK0 - ACV C14 H25 N3 O6 S CC(C)[C@H]....
31 1OBN - ASV C13 H21 N3 O6 S C=C[C@H](C....
32 3ZOI - M2W C14 H25 N3 O7 S C[C@@H]([C....
33 2VBD - V10 C13 H22 N2 O7 S2 CSC[C@@H](....
34 1W05 - W05 C12 H21 N3 O6 S C[C@H](C(=....
35 2WO7 - ASV C13 H21 N3 O6 S C=C[C@H](C....
36 1QIQ - ACC C13 H24 N3 O6 S2 CSC[C@H](C....
37 1BLZ - ACV C14 H25 N3 O6 S CC(C)[C@H]....
50% Homology Family (37)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3ZKY - WT4 C14 H25 N3 O6 S2 CSC[C@H](C....
2 2Y6F - M9F C14 H25 N3 O6 S2 CC([C@H](C....
3 1HB2 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
4 1ODN - APV C13 H19 N3 O7 S C(C[C@@H](....
5 2VBB - VAZ C13 H22 N2 O9 S2 CS[C@@H]([....
6 3ZKU - HCV C15 H27 N3 O6 S CC(C)[C@H]....
7 2VBP - VB1 C13 H23 N3 O6 S CC[C@@H](C....
8 4BB3 - KKA C10 H18 N2 O5 S C(C[C@@H](....
9 1QJE - IP1 C14 H21 N3 O6 S CC1([C@@H]....
10 1HB4 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
11 2BU9 - HFV C14 H19 F6 N3 O6 S C(C[C@@H](....
12 1W06 - W05 C12 H21 N3 O6 S C[C@H](C(=....
13 1OC1 - ASV C13 H21 N3 O6 S C=C[C@H](C....
14 1HB1 - OCV C14 H24 N2 O7 S CC(C)[C@H]....
15 2IVJ - BCV C14 H23 N3 O6 S C1CC1[C@H]....
16 2JB4 - A14 C15 H22 N2 O6 S CC1([C@@H]....
17 2VCM - M11 C15 H26 N2 O7 S CC(C)[C@H]....
18 1W04 - HCG C11 H19 N3 O6 S C(C[C@@H](....
19 1W3X - W2X C15 H24 N2 O8 S C[C@H](CO)....
20 6Y0O - ACV C14 H25 N3 O6 S CC(C)[C@H]....
21 1HB3 - SCV C14 H22 N2 O8 S CC(C)[C@H]....
22 1ODM - ASV C13 H21 N3 O6 S C=C[C@H](C....
23 2Y60 - M8F C14 H25 N3 O6 S2 CSCC[C@H](....
24 1W3V - MDZ C15 H26 N2 O7 S CC(C)[C@H]....
25 1QJF - ACS C13 H21 N3 O7 S2 C[S@](=O)C....
26 1UZW - CDH C14 H23 N3 O6 S CC(=C)[C@H....
27 2IVI - ACW C15 H25 N3 O6 S CC1(CC1)[C....
28 2VAU - V20 C13 H22 N2 O7 S2 CSC[C@H](C....
29 1W03 - HCG C11 H19 N3 O6 S C(C[C@@H](....
30 1BK0 - ACV C14 H25 N3 O6 S CC(C)[C@H]....
31 1OBN - ASV C13 H21 N3 O6 S C=C[C@H](C....
32 3ZOI - M2W C14 H25 N3 O7 S C[C@@H]([C....
33 2VBD - V10 C13 H22 N2 O7 S2 CSC[C@@H](....
34 1W05 - W05 C12 H21 N3 O6 S C[C@H](C(=....
35 2WO7 - ASV C13 H21 N3 O6 S C=C[C@H](C....
36 1QIQ - ACC C13 H24 N3 O6 S2 CSC[C@H](C....
37 1BLZ - ACV C14 H25 N3 O6 S CC(C)[C@H]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VAZ; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 VAZ 1 1
2 OCV 0.520548 0.703704
3 V10 0.480519 0.759259
4 V20 0.480519 0.759259
5 M9F 0.454545 0.740741
6 SCV 0.441558 0.703704
7 MDZ 0.441558 0.666667
8 M11 0.441558 0.666667
9 M8F 0.441558 0.678571
10 KKA 0.434783 0.673077
11 CDH 0.434211 0.637931
12 VB1 0.432432 0.685185
13 W05 0.432432 0.698113
14 WT4 0.43038 0.690909
15 ACV 0.421053 0.672727
16 W2X 0.414634 0.684211
17 HCG 0.413333 0.666667
18 M2W 0.4125 0.777778
19 HCV 0.405063 0.672727
Similar Ligands (3D)
Ligand no: 1; Ligand: VAZ; Similar ligands found: 7
No: Ligand Similarity coefficient
1 ACC 0.9481
2 ACW 0.9272
3 ACS 0.9062
4 ASV 0.9046
5 IP1 0.8925
6 BCV 0.8921
7 A14 0.8610
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ODM; Ligand: ASV; 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: 1odm.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback