scPDB - 1lkd entry

Protein Data Bank Entry:

PDB ID : 1lkd

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2002-04-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Biphenyl-2,3-diol 1,2-dioxygenase
ID:	BPHC_BURXL
AC:	P47228
Organism:	Burkholderia xenovorans
Reign:	Bacteria
TaxID:	266265
EC Number:	1.13.11.39

Chains:

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

Ligand binding site composition:

B-Factor:	15.203
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
1.354	563.625

% Hydrophobic	% Polar
55.69	44.31
According to VolSite

Ligand :

HET Code:	BP6
Formula:	C12H8Cl2O2
Molecular weight:	255.097 g/mol
DrugBank ID:	DB03259
Buried Surface Area:	72.34 %
Polar Surface area:	40.46 Å2

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

Mass center Coordinates

X	Y	Z
22.5883	22.5094	16.652

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
CL1	CG2	VAL- 148	3.41	0	Hydrophobic	false
CA5	CD1	ILE- 173	3.77	0	Hydrophobic	false
CA6	CE	MET- 175	3.99	0	Hydrophobic	false
CB2	CE	MET- 175	3.51	0	Hydrophobic	false
CB2	CE	MET- 175	3.51	0	Hydrophobic	false
CL1	CE2	PHE- 187	3.82	0	Hydrophobic	false
CA5	CE2	PHE- 187	3.49	0	Hydrophobic	false
CL1	CB	ALA- 198	4.28	0	Hydrophobic	false
DuAr	DuAr	HIS- 241	3.57	0	Aromatic Face/Face	false
CA4	CB	HIS- 241	4.02	0	Hydrophobic	false
OA2	OH	TYR- 250	2.68	160.46	H-Bond (Protein Donor)	false
CL2	CZ	TYR- 250	4.15	0	Hydrophobic	false
CA6	CB	PRO- 280	3.74	0	Hydrophobic	false
CL2	CB	PRO- 280	3.71	0	Hydrophobic	false
OA2	FE	FE2- 500	2.06	0	Metal Acceptor	false
OA3	FE	FE2- 500	2.29	0	Metal Acceptor	false