scPDB - 4cf6 entry

Protein Data Bank Entry:

PDB ID : 4cf6

Resolution :2.690 Å

Experimental Method : X-ray

Deposition Date : 2013-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P)H dehydrogenase [quinone] 1
ID:	NQO1_HUMAN
AC:	P15559
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.6.5.2

Chains:

Chain Name:	Percentage of Residues within binding site
A	45 %
B	55 %

Ligand binding site composition:

B-Factor:	43.561
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.086	749.250

% Hydrophobic	% Polar
46.40	53.60
According to VolSite

Ligand :

HET Code:	CBD
Formula:	C29H17ClN7O11S3
Molecular weight:	771.134 g/mol
DrugBank ID:	DB02633
Buried Surface Area:	48.21 %
Polar Surface area:	331.65 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	4
Rings:	6
Aromatic rings:	5
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-19.8243	26.0752	25.2339

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
O3D	OG	SER- 152	2.97	165.67	H-Bond (Protein Donor)	false
CD6	CB	SER- 152	3.71	0	Hydrophobic	false
CD6	CB	SER- 154	4.15	0	Hydrophobic	false
CB6	SD	MET- 155	4.33	0	Hydrophobic	false
CB3	CB	SER- 192	3.97	0	Hydrophobic	false
CB3	CB	HIS- 195	4.04	0	Hydrophobic	false
CL	CB	PHE- 233	3.51	0	Hydrophobic	false
C2	C1'	FAD- 1275	3.96	0	Hydrophobic	false