scPDB - 3ndr entry

Protein Data Bank Entry:

PDB ID : 3ndr

Resolution :2.880 Å

Experimental Method : X-ray

Deposition Date : 2010-06-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxal 4-dehydrogenase
ID:	PLDH_RHILO
AC:	Q988B7
Organism:	Rhizobium loti
Reign:	Bacteria
TaxID:	266835
EC Number:	1.1.1.107

Chains:

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

Ligand binding site composition:

B-Factor:	25.313
Number of residues:	47
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.763	965.250

% Hydrophobic	% Polar
55.24	44.76
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	73.51 %
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
21.45	12.2802	44.7742

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
O2A	NE2	GLN- 17	3.39	138.94	H-Bond (Protein Donor)	false
C3B	CG	GLN- 17	4.16	0	Hydrophobic	false
O2N	N	ILE- 19	2.92	167.02	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 19	3.72	0	Hydrophobic	false
O3B	OD2	ASP- 38	2.89	174.04	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 38	2.66	160.36	H-Bond (Ligand Donor)	false
N3A	N	ILE- 39	3.31	135.49	H-Bond (Protein Donor)	false
N6A	OD2	ASP- 61	2.64	149.92	H-Bond (Ligand Donor)	false
N1A	N	ILE- 62	2.91	160.97	H-Bond (Protein Donor)	false
O3D	O	ASN- 88	2.62	157.64	H-Bond (Ligand Donor)	false
C3D	CB	SER- 90	3.91	0	Hydrophobic	false
C2D	CG2	VAL- 92	3.91	0	Hydrophobic	false
C4D	CG2	ILE- 139	3.62	0	Hydrophobic	false
C5N	CB	SER- 141	3.96	0	Hydrophobic	false
O2D	OH	TYR- 154	2.95	139.97	H-Bond (Protein Donor)	false
O3D	NZ	LYS- 158	3.26	155.65	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 158	2.85	136.87	H-Bond (Protein Donor)	false
C5N	CB	PRO- 184	3.68	0	Hydrophobic	false
O7N	N	ILE- 187	2.67	157.61	H-Bond (Protein Donor)	false
O1N	OG	SER- 189	2.87	150.56	H-Bond (Protein Donor)	false