scPDB - 4bb3 entry

Protein Data Bank Entry:

PDB ID : 4bb3

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2012-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Isopenicillin N synthase
ID:	IPNS_EMENI
AC:	P05326
Organism:	Emericella nidulans
Reign:	Eukaryota
TaxID:	227321
EC Number:	1.21.3.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	12.766
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE

Cavity properties

Ligandability	Volume (Å3)
1.513	1211.625

% Hydrophobic	% Polar
56.82	43.18
According to VolSite

Ligand :

HET Code:	KKA
Formula:	C10H17N2O5S
Molecular weight:	277.317 g/mol
DrugBank ID:	-
Buried Surface Area:	56.79 %
Polar Surface area:	175.8 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
12.3344	39.1168	5.29622

Binding mode :

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
O3	NH2	ARG- 87	2.86	177.36	H-Bond (Protein Donor)	false
O4	NE	ARG- 87	2.85	173.5	H-Bond (Protein Donor)	false
O3	CZ	ARG- 87	3.7	0	Ionic (Protein Cationic)	false
O4	CZ	ARG- 87	3.7	0	Ionic (Protein Cationic)	false
O3	OG	SER- 183	2.72	166.04	H-Bond (Protein Donor)	false
S	CD1	PHE- 211	3.78	0	Hydrophobic	false
C7	CB	PHE- 211	3.98	0	Hydrophobic	false
C2	CE2	PHE- 285	3.81	0	Hydrophobic	false
C1	CD2	LEU- 321	3.98	0	Hydrophobic	false
C3	CD2	LEU- 324	3.89	0	Hydrophobic	false
C6	CD2	LEU- 324	3.94	0	Hydrophobic	false
S	CB	ASN- 328	3.5	0	Hydrophobic	false
O1	FE	FE- 1332	2.26	0	Metal Acceptor	false
N1	O	HOH- 2212	3.08	149.36	H-Bond (Ligand Donor)	false