scPDB - 2y6f entry

Protein Data Bank Entry:

PDB ID : 2y6f

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2011-01-21

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:	14.524
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE

Cavity properties

Ligandability	Volume (Å3)
1.371	961.875

% Hydrophobic	% Polar
55.79	44.21
According to VolSite

Ligand :

HET Code:	M9F
Formula:	C14H24N3O6S2
Molecular weight:	394.487 g/mol
DrugBank ID:	-
Buried Surface Area:	63.44 %
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:	12

Mass center Coordinates

X	Y	Z
10.6691	39.25	4.83592

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	NH2	ARG- 87	2.83	176.19	H-Bond (Protein Donor)	false
OXT	NE	ARG- 87	2.8	159.83	H-Bond (Protein Donor)	false
O	CZ	ARG- 87	3.66	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 87	3.65	0	Ionic (Protein Cationic)	false
O	OG	SER- 183	2.78	164.24	H-Bond (Protein Donor)	false
OAQ	OH	TYR- 189	2.58	170.74	H-Bond (Protein Donor)	false
CAE	CE2	PHE- 211	3.5	0	Hydrophobic	false
CAN	CD2	LEU- 231	3.36	0	Hydrophobic	false
CAN	CG2	VAL- 272	3.73	0	Hydrophobic	false
OAR	OG	SER- 281	2.76	170.12	H-Bond (Protein Donor)	false
SAF	CE1	PHE- 285	3.91	0	Hydrophobic	false
CAS	CE2	PHE- 285	4.11	0	Hydrophobic	false
CAT	CD2	LEU- 321	4.23	0	Hydrophobic	false
CB	CD2	LEU- 321	3.83	0	Hydrophobic	false
CAT	CD1	LEU- 324	3.89	0	Hydrophobic	false
CAE	CD1	LEU- 324	4.23	0	Hydrophobic	false
OAR	O	HOH- 2287	2.85	179.97	H-Bond (Protein Donor)	false