Receptor
PDB id Resolution Class Description Source Keywords
4BB3 1.4 Å EC: 1.21.3.1 ISOPENICILLIN N SYNTHASE WITH THE DIPEPTIDE SUBSTRATE ANALOG ASPERGILLUS NIDULANS FGSC A4 ANTIBIOTIC BIOSYNTHESIS B-LACTAM ANTIBIOTIC OXIDOREDUCTASEOXYGENASE PENICILLIN BIOSYNTHESIS
Ref.: THE CRYSTAL STRUCTURE OF ISOPENICILLIN N SYNTHASE W DIPEPTIDE SUBSTRATE ANALOGUE. ARCH.BIOCHEM.BIOPHYS. V. 530 48 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1334;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
FE A:1332;
 Part of Protein;
 none;
 submit data
55.845 Fe [Fe+3...
KKA A:1333;
 Valid;
 none;
 submit data
278.325 C10 H18 N2 O5 S C(C[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: KKA; Similar ligands found: 37
No: Ligand ECFP6 Tc MDL keys Tc
1 KKA 1 1
2 WT4 0.62069 0.853659
3 HCV 0.614035 0.875
4 VB1 0.611111 0.897436
5 CYK 0.591837 0.756098
6 M8F 0.586207 0.833333
7 HCG 0.581818 0.921053
8 W05 0.581818 0.921053
9 ASV 0.578947 0.897436
10 ACV 0.561404 0.875
11 OCV 0.559322 0.829268
12 BCV 0.551724 0.897436
13 CDH 0.551724 0.813953
14 HFV 0.52459 0.795455
15 M9F 0.52459 0.833333
16 M2W 0.516129 0.795455
17 ACW 0.516129 0.795455
18 SCV 0.508197 0.704545
19 V20 0.507937 0.772727
20 V10 0.507937 0.772727
21 KSN 0.480769 0.885714
22 3GC 0.470588 0.971429
23 MDZ 0.460317 0.738095
24 M11 0.460317 0.738095
25 26P 0.446809 0.702703
26 UN1 0.444444 0.714286
27 11C 0.444444 0.714286
28 MHI 0.442623 0.815789
29 VAZ 0.434783 0.673077
30 HCS 0.428571 0.685714
31 W2X 0.426471 0.717391
32 16E 0.418182 0.756757
33 REZ 0.418182 0.789474
34 3KS 0.402985 0.794872
35 C6L 0.4 0.72093
36 2NP 0.4 0.65
37 GSH 0.4 0.894737
Similar Ligands (3D)
Ligand no: 1; Ligand: KKA; Similar ligands found: 1
No: Ligand Similarity coefficient
1 PHE LEU 0.8590
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
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