scPDB - 4g8c entry

Protein Data Bank Entry:

PDB ID : 4g8c

Resolution :1.110 Å

Experimental Method : X-ray

Deposition Date : 2012-07-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alpha/beta hydrolase fold protein
ID:	D2J2T6_9RHIZ
AC:	D2J2T6
Organism:	Ochrobactrum sp. T63
Reign:	Bacteria
TaxID:	680275
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.705
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.495	411.750

% Hydrophobic	% Polar
73.77	26.23
According to VolSite

Ligand :

HET Code:	C6L
Formula:	C10H18NO4
Molecular weight:	216.254 g/mol
DrugBank ID:	DB07532
Buried Surface Area:	67.68 %
Polar Surface area:	89.46 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-1.06507	-22.5248	45.8615

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
O4	ND2	ASN- 33	2.9	170.85	H-Bond (Protein Donor)	false
O2	N	ASN- 33	2.81	169.27	H-Bond (Protein Donor)	false
C10	CE	MET- 77	4.31	0	Hydrophobic	false
C7	CE	MET- 77	3.88	0	Hydrophobic	false
C2	CB	SER- 102	4.31	0	Hydrophobic	false
C6	CB	LEU- 103	4.07	0	Hydrophobic	false
O2	N	LEU- 103	2.84	163.68	H-Bond (Protein Donor)	false
C8	CZ	PHE- 138	4.03	0	Hydrophobic	false
C1	CB	ALA- 147	4.39	0	Hydrophobic	false
C6	CE	MET- 188	4.36	0	Hydrophobic	false
C7	SD	MET- 188	3.81	0	Hydrophobic	false
C9	CD1	PHE- 189	3.59	0	Hydrophobic	false
C10	CD1	PHE- 192	3.87	0	Hydrophobic	false
C1	CG	PHE- 221	3.8	0	Hydrophobic	false
N1	O	HOH- 513	3.21	163.6	H-Bond (Ligand Donor)	false