scPDB - 1nvm entry

Protein Data Bank Entry:

PDB ID : 1nvm

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2003-02-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Acetaldehyde dehydrogenase
ID:	ACDH_PSEUF
AC:	Q52060
Organism:	Pseudomonas sp.
Reign:	Bacteria
TaxID:	79676
EC Number:	1.2.1.10

Chains:

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

Ligand binding site composition:

B-Factor:	31.126
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.332	614.250

% Hydrophobic	% Polar
54.95	45.05
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	67.11 %
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
32.487	26.257	105.252

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	N	SER- 12	3.07	128.02	H-Bond (Protein Donor)	false
O2A	N	ASN- 14	3.1	163.5	H-Bond (Protein Donor)	false
O2N	N	ILE- 15	2.9	172.39	H-Bond (Protein Donor)	false
C5D	CB	ILE- 15	4.2	0	Hydrophobic	false
C3N	CG1	ILE- 15	3.5	0	Hydrophobic	false
C4N	CD1	ILE- 15	3.37	0	Hydrophobic	false
C1B	CG1	ILE- 38	4.36	0	Hydrophobic	false
C1B	CG2	THR- 79	4.32	0	Hydrophobic	false
C4N	CB	CYS- 132	3.41	0	Hydrophobic	false
N7N	O	SER- 163	3.1	166.31	H-Bond (Ligand Donor)	false
O1N	N	GLY- 165	2.99	151.24	H-Bond (Protein Donor)	false
O1A	N	GLY- 167	2.85	162.87	H-Bond (Protein Donor)	false
O3	N	GLY- 167	3.41	121.04	H-Bond (Protein Donor)	false
O1N	OG1	THR- 168	2.79	140.76	H-Bond (Protein Donor)	false
C2D	CB	THR- 168	3.94	0	Hydrophobic	false
N7N	OG1	THR- 168	3.09	128.38	H-Bond (Ligand Donor)	false
O3D	OD1	ASN- 171	2.83	160.67	H-Bond (Ligand Donor)	false
O2D	ND2	ASN- 171	2.98	166.58	H-Bond (Protein Donor)	false
O7N	ND2	ASN- 290	2.91	163.4	H-Bond (Protein Donor)	false
C5N	CB	MET- 294	3.57	0	Hydrophobic	false
O2N	O	HOH- 3602	2.98	179.97	H-Bond (Protein Donor)	false