scPDB - 2vhx entry

Protein Data Bank Entry:

PDB ID : 2vhx

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-11-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alanine dehydrogenase
ID:	DHA_MYCTU
AC:	P9WQB1
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	1.4.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	11.009
Number of residues:	55
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.929	668.250

% Hydrophobic	% Polar
53.54	46.46
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	69.98 %
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
-41.2447	12.859	-34.4543

Binding mode :

What is Poseview ?

2D View
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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
C2D	CD1	LEU- 130	3.97	0	Hydrophobic	false
C5N	CD1	LEU- 130	4.21	0	Hydrophobic	false
C5N	CB	MET- 133	3.82	0	Hydrophobic	false
O1N	OG	SER- 134	2.64	158.03	H-Bond (Protein Donor)	false
C4N	CB	ALA- 137	3.61	0	Hydrophobic	false
O2A	N	THR- 178	3.08	166.92	H-Bond (Protein Donor)	false
O2N	N	ALA- 179	2.78	155.14	H-Bond (Protein Donor)	false
C5D	CB	ALA- 179	4.23	0	Hydrophobic	false
O3B	OD2	ASP- 198	2.72	168.3	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 198	2.67	166.96	H-Bond (Ligand Donor)	false
O3B	NZ	LYS- 203	2.81	147.02	H-Bond (Protein Donor)	false
C1B	CG1	VAL- 239	4.46	0	Hydrophobic	false
C5B	CB	LEU- 240	3.74	0	Hydrophobic	false
C3D	CB	LEU- 240	3.86	0	Hydrophobic	false
O4B	N	LEU- 240	3.31	157.64	H-Bond (Protein Donor)	false
C3N	CG2	ILE- 267	4.07	0	Hydrophobic	false
N7N	O	ILE- 267	2.97	172.93	H-Bond (Ligand Donor)	false
O3D	OD2	ASP- 270	3.09	170.6	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 270	3.01	158.55	H-Bond (Ligand Donor)	false
N7N	O	VAL- 298	3.01	171.46	H-Bond (Ligand Donor)	false
O7N	N	MET- 301	2.68	134.37	H-Bond (Protein Donor)	false
C4N	CG	PRO- 302	4.15	0	Hydrophobic	false
O2B	O	HOH- 2131	3.02	179.99	H-Bond (Protein Donor)	false
O2N	O	HOH- 2252	2.7	179.96	H-Bond (Protein Donor)	false