scPDB - 2vbd entry

Protein Data Bank Entry:

PDB ID : 2vbd

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-09-10

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:	11.768
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.574	1002.375

% Hydrophobic	% Polar
60.94	39.06
According to VolSite

Ligand :

HET Code:	V10
Formula:	C13H21N2O7S2
Molecular weight:	381.445 g/mol
DrugBank ID:	-
Buried Surface Area:	63.19 %
Polar Surface area:	227.39 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
10.8254	38.3684	5.85321

Binding mode :

What is Poseview ?

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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
O	CZ	ARG- 87	3.56	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 87	3.69	0	Ionic (Protein Cationic)	false
O	NE	ARG- 87	2.72	163.32	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 87	2.86	176.05	H-Bond (Protein Donor)	false
SAQ	CG1	VAL- 100	4.38	0	Hydrophobic	false
CAA	CG2	VAL- 100	4.14	0	Hydrophobic	false
OXT	OG	SER- 183	2.58	167.69	H-Bond (Protein Donor)	false
CAX	CD1	ILE- 187	3.8	0	Hydrophobic	false
CAA	CD1	ILE- 187	4.05	0	Hydrophobic	false
OAD	OH	TYR- 189	2.55	168.26	H-Bond (Protein Donor)	false
CAN	CZ	TYR- 189	4.2	0	Hydrophobic	false
CAK	CE2	PHE- 211	3.45	0	Hydrophobic	false
CAN	CG	PHE- 211	3.74	0	Hydrophobic	false
SAQ	CD1	PHE- 211	3.68	0	Hydrophobic	false
SAI	CE2	PHE- 285	3.72	0	Hydrophobic	false
CAJ	CE1	PHE- 285	3.95	0	Hydrophobic	false
CB	CD2	LEU- 321	3.86	0	Hydrophobic	false
CAL	CD2	LEU- 321	4.35	0	Hydrophobic	false
CAL	CD1	LEU- 324	3.84	0	Hydrophobic	false
CAK	CD1	LEU- 324	4.15	0	Hydrophobic	false
SAQ	CG2	THR- 331	3.61	0	Hydrophobic	false
CAA	CB	THR- 331	3.72	0	Hydrophobic	false
OAD	O	HOH- 2213	2.87	179.97	H-Bond (Protein Donor)	false