scPDB - 2y60 entry

Protein Data Bank Entry:

PDB ID : 2y60

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2011-01-19

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:	9.331
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE

Cavity properties

Ligandability	Volume (Å3)
1.709	884.250

% Hydrophobic	% Polar
65.65	34.35
According to VolSite

Ligand :

HET Code:	M8F
Formula:	C14H24N3O6S2
Molecular weight:	394.487 g/mol
DrugBank ID:	-
Buried Surface Area:	65.73 %
Polar Surface area:	230.2 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
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
10.4049	37.9214	4.67084

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
O4	NE	ARG- 87	2.86	169.1	H-Bond (Protein Donor)	false
O3	NH2	ARG- 87	2.78	178.98	H-Bond (Protein Donor)	false
O4	CZ	ARG- 87	3.69	0	Ionic (Protein Cationic)	false
O3	CZ	ARG- 87	3.64	0	Ionic (Protein Cationic)	false
O3	OG	SER- 183	2.66	164.28	H-Bond (Protein Donor)	false
C18	CD1	ILE- 187	4.33	0	Hydrophobic	false
O24	OH	TYR- 189	2.66	173.9	H-Bond (Protein Donor)	false
C12	CE2	PHE- 211	3.41	0	Hydrophobic	false
C18	CD1	LEU- 223	4.25	0	Hydrophobic	false
C21	CD2	LEU- 223	4.2	0	Hydrophobic	false
C21	CD2	LEU- 231	3.51	0	Hydrophobic	false
C21	CG2	VAL- 272	4.22	0	Hydrophobic	false
O23	OG	SER- 281	2.69	166.81	H-Bond (Protein Donor)	false
C18	CG	PRO- 283	4.38	0	Hydrophobic	false
S13	CE1	PHE- 285	3.72	0	Hydrophobic	false
C6	CE2	PHE- 285	3.82	0	Hydrophobic	false
C7	CD2	LEU- 321	4.29	0	Hydrophobic	false
C5	CD2	LEU- 321	3.85	0	Hydrophobic	false
C7	CD2	LEU- 324	3.87	0	Hydrophobic	false
O23	O	HOH- 2388	2.65	179.98	H-Bond (Protein Donor)	false