scPDB - 2vbp entry

Protein Data Bank Entry:

PDB ID : 2vbp

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2007-09-14

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:	10.788
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.652	712.125

% Hydrophobic	% Polar
64.45	35.55
According to VolSite

Ligand :

HET Code:	VB1
Formula:	C13H22N3O6S
Molecular weight:	348.395 g/mol
DrugBank ID:	-
Buried Surface Area:	63.01 %
Polar Surface area:	204.89 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
8.39348	-2.18852	8.61339

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
O19	NH2	ARG- 87	2.77	176.6	H-Bond (Protein Donor)	false
O20	NE	ARG- 87	2.81	165.67	H-Bond (Protein Donor)	false
O19	CZ	ARG- 87	3.6	0	Ionic (Protein Cationic)	false
O20	CZ	ARG- 87	3.66	0	Ionic (Protein Cationic)	false
C32	CG2	VAL- 100	4.18	0	Hydrophobic	false
O19	OG	SER- 183	2.7	163.42	H-Bond (Protein Donor)	false
C33	CZ	TYR- 189	4.02	0	Hydrophobic	false
C16	CE2	PHE- 211	3.47	0	Hydrophobic	false
C33	CD1	PHE- 211	3.9	0	Hydrophobic	false
S17	CZ	PHE- 285	3.7	0	Hydrophobic	false
C4	CE2	PHE- 285	4.09	0	Hydrophobic	false
C3	CD2	LEU- 321	3.89	0	Hydrophobic	false
C7	CD2	LEU- 321	4.23	0	Hydrophobic	false
C7	CD2	LEU- 324	4.04	0	Hydrophobic	false
C16	CD2	LEU- 324	4.27	0	Hydrophobic	false
C32	CG2	THR- 331	3.62	0	Hydrophobic	false
O43	O	HOH- 2333	2.97	153.55	H-Bond (Protein Donor)	false