scPDB - 3pvr entry

Protein Data Bank Entry:

PDB ID : 3pvr

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2010-12-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1,2-phenylacetyl-CoA epoxidase, subunit A
ID:	PAAA_ECOLI
AC:	P76077
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.14.13.149

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	27.510
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.943	965.250

% Hydrophobic	% Polar
40.91	59.09
According to VolSite

Ligand :

HET Code:	BYC
Formula:	C28H36N7O17P3S
Molecular weight:	867.608 g/mol
DrugBank ID:	-
Buried Surface Area:	70.18 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
-35.5518	51.4086	-32.6322

Binding mode :

What is Poseview ?

2D View
3D View

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
O4A	NH2	ARG- 33	3.22	140.87	H-Bond (Protein Donor)	false
O4A	NH1	ARG- 33	2.97	154.52	H-Bond (Protein Donor)	false
O9A	NH1	ARG- 33	2.88	164.91	H-Bond (Protein Donor)	false
O4A	CZ	ARG- 33	3.54	0	Ionic (Protein Cationic)	false
O9A	CZ	ARG- 33	3.86	0	Ionic (Protein Cationic)	false
CAP	CG	GLN- 34	4.39	0	Hydrophobic	false
O9A	NE2	GLN- 37	2.9	161.61	H-Bond (Protein Donor)	false
C2P	CB	SER- 41	3.64	0	Hydrophobic	false
C6B	CG	GLU- 72	3.56	0	Hydrophobic	false
C1D	CD	LYS- 103	3.81	0	Hydrophobic	false
O7A	NZ	LYS- 103	2.88	166.23	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 103	2.88	0	Ionic (Protein Cationic)	false
N1A	N	SER- 106	2.73	160.21	H-Bond (Protein Donor)	false
N6A	OG	SER- 106	3.09	128.28	H-Bond (Ligand Donor)	false
S1P	CE2	PHE- 108	4.39	0	Hydrophobic	false
C2B	CZ	PHE- 108	3.33	0	Hydrophobic	false
C4B	CG1	VAL- 125	3.97	0	Hydrophobic	false
S1P	CB	ALA- 129	3.79	0	Hydrophobic	false
C3B	CB	ALA- 129	4.21	0	Hydrophobic	false
O9P	ND2	ASN- 132	3.09	148.27	H-Bond (Protein Donor)	false
N6A	O	MET- 193	3.11	130.26	H-Bond (Ligand Donor)	false
S1P	CE	MET- 194	4.3	0	Hydrophobic	false
C5D	CG	PRO- 197	4.06	0	Hydrophobic	false
O2A	OG	SER- 202	2.72	160.75	H-Bond (Protein Donor)	false
C5D	CG	PRO- 203	4.35	0	Hydrophobic	false
O1A	N	ASN- 204	2.94	165.39	H-Bond (Protein Donor)	false
O1A	ND2	ASN- 204	3.2	127.95	H-Bond (Protein Donor)	false
O3A	ND2	ASN- 204	3.27	167.08	H-Bond (Protein Donor)	false
O8A	ND2	ASN- 204	3.13	163.46	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 214	3.82	0	Ionic (Protein Cationic)	false
O5A	NZ	LYS- 214	2.84	0	Ionic (Protein Cationic)	false
O5A	NZ	LYS- 214	2.84	167.15	H-Bond (Protein Donor)	false
O6A	NZ	LYS- 214	3.44	123.31	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 218	3.03	155.64	H-Bond (Protein Donor)	false