scPDB - 3vdq entry

Protein Data Bank Entry:

PDB ID : 3vdq

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-01-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-hydroxybutyrate dehydrogenase
ID:	D0VWQ0_ALCFA
AC:	D0VWQ0
Organism:	Alcaligenes faecalis
Reign:	Bacteria
TaxID:	511
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.580
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.126	671.625

% Hydrophobic	% Polar
43.72	56.28
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	72.52 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
16.2775	61.3004	-16.138

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	OG1	THR- 13	2.79	121.97	H-Bond (Ligand Donor)	false
O2N	N	ILE- 16	3.1	156.57	H-Bond (Protein Donor)	false
C5D	CB	ILE- 16	4.06	0	Hydrophobic	false
C4D	CD1	ILE- 16	4.32	0	Hydrophobic	false
C3N	CD1	ILE- 16	4.01	0	Hydrophobic	false
N6A	OD2	ASP- 63	2.86	127.23	H-Bond (Ligand Donor)	false
N1A	N	LEU- 64	3.2	147.41	H-Bond (Protein Donor)	false
O3D	O	ASN- 90	2.66	146.77	H-Bond (Ligand Donor)	false
C4D	CG2	ILE- 140	3.9	0	Hydrophobic	false
C5N	CB	SER- 142	3.69	0	Hydrophobic	false
O2D	OH	TYR- 155	2.94	168	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 159	3.11	146.92	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 159	2.66	134.98	H-Bond (Protein Donor)	false
C5N	CB	PRO- 185	3.7	0	Hydrophobic	false
C3N	CB	VAL- 188	4.43	0	Hydrophobic	false
O7N	N	VAL- 188	2.64	146.21	H-Bond (Protein Donor)	false
N7N	O	VAL- 188	3.07	131.67	H-Bond (Ligand Donor)	false
O1N	OG1	THR- 190	2.64	169.08	H-Bond (Protein Donor)	false
C2D	CD1	LEU- 192	4.18	0	Hydrophobic	false
O2N	O	HOH- 441	2.74	179.98	H-Bond (Protein Donor)	false