scPDB - 3nhl entry

Protein Data Bank Entry:

PDB ID : 3nhl

Resolution :1.570 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	52 %
B	48 %

Ligand binding site composition:

B-Factor:	26.611
Number of residues:	28
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.974	536.625

% Hydrophobic	% Polar
54.09	45.91
According to VolSite

Ligand :

HET Code:	YTR
Formula:	C13H15NO3
Molecular weight:	233.263 g/mol
DrugBank ID:	-
Buried Surface Area:	66.23 %
Polar Surface area:	38.77 Å2

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

Mass center Coordinates

X	Y	Z
-3.37653	-7.03724	-16.0415

Binding mode :

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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
C13	CE3	TRP- 105	4.27	0	Hydrophobic	false
C17	CZ2	TRP- 105	4.24	0	Hydrophobic	false
C1	CZ3	TRP- 105	3.31	0	Hydrophobic	false
C13	CE1	PHE- 106	3.26	0	Hydrophobic	false
C15	CZ	PHE- 126	4.4	0	Hydrophobic	false
C17	CE1	PHE- 126	3.41	0	Hydrophobic	false
O11	ND2	ASN- 161	2.99	154.39	H-Bond (Protein Donor)	false
C13	CD1	PHE- 178	3.45	0	Hydrophobic	false
C2	CZ	PHE- 178	3.5	0	Hydrophobic	false
C4	C1'	FAD- 232	4.39	0	Hydrophobic	false
C15	C1'	FAD- 232	3.92	0	Hydrophobic	false
C17	C7	FAD- 232	3.34	0	Hydrophobic	false