scPDB - 3v1m entry

Protein Data Bank Entry:

PDB ID : 3v1m

Resolution :1.920 Å

Experimental Method : X-ray

Deposition Date : 2011-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase
ID:	BPHD_BURXL
AC:	P47229
Organism:	Burkholderia xenovorans
Reign:	Bacteria
TaxID:	266265
EC Number:	3.7.1.8

Chains:

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

Ligand binding site composition:

B-Factor:	22.254
Number of residues:	34
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.684	502.875

% Hydrophobic	% Polar
75.17	24.83
According to VolSite

Ligand :

HET Code:	HPK
Formula:	C12H9O4
Molecular weight:	217.197 g/mol
DrugBank ID:	DB07911
Buried Surface Area:	68.92 %
Polar Surface area:	74.27 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-0.179062	14.5688	-17.8217

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
OA4	N	GLY- 42	2.7	160.89	H-Bond (Protein Donor)	false
OA2	N	GLY- 43	2.95	166.56	H-Bond (Protein Donor)	false
CB1	CB	ALA- 112	3.91	0	Hydrophobic	false
CB2	CB	MET- 113	4.27	0	Hydrophobic	false
OA4	N	MET- 113	2.87	150.78	H-Bond (Protein Donor)	false
CB5	CD1	ILE- 153	3.2	0	Hydrophobic	false
OA3	NH2	ARG- 190	3.14	137.7	H-Bond (Protein Donor)	false
OA1	NH1	ARG- 190	2.87	151.73	H-Bond (Protein Donor)	false
OA1	NH2	ARG- 190	3.28	133.05	H-Bond (Protein Donor)	false
OA1	CZ	ARG- 190	3.49	0	Ionic (Protein Cationic)	false
CB3	CD1	LEU- 213	3.77	0	Hydrophobic	false
CB5	CG2	VAL- 240	3.59	0	Hydrophobic	false
OA2	O	HOH- 399	2.88	140.93	H-Bond (Protein Donor)	false