scPDB - 2vqd entry

Protein Data Bank Entry:

PDB ID : 2vqd

Resolution :2.410 Å

Experimental Method : X-ray

Deposition Date : 2008-03-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Biotin carboxylase
ID:	ACCC_PSEAE
AC:	P37798
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	6.3.4.14

Chains:

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

Ligand binding site composition:

B-Factor:	36.951
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.031	813.375

% Hydrophobic	% Polar
42.32	57.68
According to VolSite

Ligand :

HET Code:	AP2
Formula:	C11H14N5O9P2
Molecular weight:	422.204 g/mol
DrugBank ID:	DB03148
Buried Surface Area:	78.37 %
Polar Surface area:	251.48 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
0.491111	31.0086	9.91063

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
O3B	NZ	LYS- 116	3.33	148.52	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 116	2.99	152.49	H-Bond (Protein Donor)	false
O3B	NZ	LYS- 116	3.33	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 116	2.99	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 159	2.8	166.39	H-Bond (Protein Donor)	false
N7	NZ	LYS- 159	3.09	133.56	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 159	2.8	0	Ionic (Protein Cationic)	false
O2B	N	GLY- 166	2.61	138.34	H-Bond (Protein Donor)	false
C3A	SD	MET- 169	4.23	0	Hydrophobic	false
C1'	CE	MET- 169	4.06	0	Hydrophobic	false
N6	OE2	GLU- 201	3.25	166.89	H-Bond (Ligand Donor)	false
N6	O	LYS- 202	2.86	161.34	H-Bond (Ligand Donor)	false
N1	N	LEU- 204	3.01	147.91	H-Bond (Protein Donor)	false
O3'	NE2	GLN- 233	2.97	152.03	H-Bond (Protein Donor)	false
O2'	OE1	GLN- 233	2.75	138.99	H-Bond (Ligand Donor)	false
C4'	CB	HIS- 236	3.9	0	Hydrophobic	false
C2'	CD2	LEU- 278	4.34	0	Hydrophobic	false
C3'	CD1	ILE- 287	4.24	0	Hydrophobic	false
C2'	CD1	ILE- 437	3.6	0	Hydrophobic	false
O1B	MG	MG- 1449	2.01	0	Metal Acceptor	false
O2A	MG	MG- 1449	2.37	0	Metal Acceptor	false