scPDB - 3nhf entry

Protein Data Bank Entry:

PDB ID : 3nhf

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-06-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribosyldihydronicotinamide dehydrogenase [quinone]
ID:	NQO2_HUMAN
AC:	P16083
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	56 %
B	44 %

Ligand binding site composition:

B-Factor:	19.756
Number of residues:	26
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.160	752.625

% Hydrophobic	% Polar
49.78	50.22
According to VolSite

Ligand :

HET Code:	VVV
Formula:	C13H15NO4
Molecular weight:	249.262 g/mol
DrugBank ID:	-
Buried Surface Area:	64.8 %
Polar Surface area:	56.79 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
-4.05456	-6.65311	-15.5712

Binding mode :

What is Poseview ?

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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
C14	CZ2	TRP- 105	3.36	0	Hydrophobic	false
C18	CE3	TRP- 105	3.81	0	Hydrophobic	false
C18	CE1	PHE- 106	3.55	0	Hydrophobic	false
C14	CZ	PHE- 126	3.48	0	Hydrophobic	false
O16	ND2	ASN- 161	2.91	153.38	H-Bond (Protein Donor)	false
C18	CD1	PHE- 178	3.69	0	Hydrophobic	false
C4	CZ	PHE- 178	3.5	0	Hydrophobic	false
C1	C1'	FAD- 233	4.05	0	Hydrophobic	false
C12	C1'	FAD- 233	3.51	0	Hydrophobic	false
C14	C6	FAD- 233	3.44	0	Hydrophobic	false