scPDB - 2vcm entry

Protein Data Bank Entry:

PDB ID : 2vcm

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2007-09-25

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:	15.328
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.671	648.000

% Hydrophobic	% Polar
65.10	34.90
According to VolSite

Ligand :

HET Code:	M11
Formula:	C15H25N2O7S
Molecular weight:	377.433 g/mol
DrugBank ID:	-
Buried Surface Area:	65.84 %
Polar Surface area:	202.09 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
8.87284	-2.56908	7.79796

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
O20	CZ	ARG- 87	3.69	0	Ionic (Protein Cationic)	false
O19	CZ	ARG- 87	3.63	0	Ionic (Protein Cationic)	false
O20	NH2	ARG- 87	2.88	176.12	H-Bond (Protein Donor)	false
O19	NE	ARG- 87	2.76	175.09	H-Bond (Protein Donor)	false
O20	OG	SER- 183	2.67	167.11	H-Bond (Protein Donor)	false
C4	CG2	VAL- 185	4.48	0	Hydrophobic	false
C30	CD1	ILE- 187	4.2	0	Hydrophobic	false
O43	OH	TYR- 189	2.81	174.26	H-Bond (Protein Donor)	false
C25	CZ	PHE- 211	3.38	0	Hydrophobic	false
CAV	CE2	PHE- 211	4.18	0	Hydrophobic	false
C33	CD2	LEU- 223	3.72	0	Hydrophobic	false
C37	CD2	LEU- 231	4.43	0	Hydrophobic	false
C33	CD2	LEU- 231	3.8	0	Hydrophobic	false
C37	CG2	VAL- 272	4.07	0	Hydrophobic	false
O42	OG	SER- 281	2.75	173.5	H-Bond (Protein Donor)	false
S17	CZ	PHE- 285	3.65	0	Hydrophobic	false
C4	CE1	PHE- 285	4	0	Hydrophobic	false
C7	CD2	LEU- 321	4.36	0	Hydrophobic	false
C3	CD2	LEU- 321	3.92	0	Hydrophobic	false
C7	CD1	LEU- 324	3.94	0	Hydrophobic	false
C25	CD1	LEU- 324	4.13	0	Hydrophobic	false
O42	O	HOH- 2271	2.63	179.96	H-Bond (Protein Donor)	false