scPDB - 1omo entry

Protein Data Bank Entry:

PDB ID : 1omo

Resolution :2.320 Å

Experimental Method : X-ray

Deposition Date : 2003-02-25

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:	ALADH_ARCFU
AC:	O28608
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.048
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.543	681.750

% Hydrophobic	% Polar
34.16	65.84
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	53.15 %
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
29.3713	20.274	10.9596

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
C4N	CG2	THR- 109	3.59	0	Hydrophobic	false
O2A	OG1	THR- 135	3.25	159.06	H-Bond (Protein Donor)	false
O2A	N	THR- 135	3.31	164.33	H-Bond (Protein Donor)	false
O1N	N	GLN- 136	3.24	134.05	H-Bond (Protein Donor)	false
O2B	OD2	ASP- 157	3.37	167.74	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 157	3.45	121.77	H-Bond (Ligand Donor)	false
C3D	CB	PRO- 196	3.83	0	Hydrophobic	false
C3N	CG2	ILE- 216	4.32	0	Hydrophobic	false
O3D	O	GLY- 217	2.85	149.27	H-Bond (Ligand Donor)	false
C2D	CB	ASP- 219	4.04	0	Hydrophobic	false
O3D	NZ	LYS- 223	3.42	133.84	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 223	3.42	151.94	H-Bond (Protein Donor)	false
O7N	OG	SER- 290	3.29	130.23	H-Bond (Protein Donor)	false
N7N	O	SER- 290	2.56	123.5	H-Bond (Ligand Donor)	false
O1N	O	HOH- 685	3.18	179.95	H-Bond (Protein Donor)	false