scPDB - 1kbo entry

Protein Data Bank Entry:

PDB ID : 1kbo

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2001-11-06

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
B	48 %
D	52 %

Ligand binding site composition:

B-Factor:	32.540
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.265	813.375

% Hydrophobic	% Polar
45.64	54.36
According to VolSite

Ligand :

HET Code:	340
Formula:	C18H17NO4
Molecular weight:	311.332 g/mol
DrugBank ID:	DB03626
Buried Surface Area:	73.85 %
Polar Surface area:	57.53 Å2

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

Mass center Coordinates

X	Y	Z
-28.6041	-32.3273	-27.387

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
C45	CG	PRO- 68	3.48	0	Hydrophobic	false
C12	CZ2	TRP- 105	3.38	0	Hydrophobic	false
C37	CZ3	TRP- 105	4.23	0	Hydrophobic	false
C37	CE1	PHE- 106	3.49	0	Hydrophobic	false
C12	CZ	TYR- 126	3.87	0	Hydrophobic	false
DuAr	DuAr	TYR- 128	3.99	0	Aromatic Face/Face	false
C26	CB	TYR- 128	3.95	0	Hydrophobic	false
C26	SD	MET- 131	3.45	0	Hydrophobic	false
C25	CE	MET- 154	3.58	0	Hydrophobic	false
C19	CZ	PHE- 178	4.47	0	Hydrophobic	false
C37	CZ	PHE- 178	3.46	0	Hydrophobic	false
C27	CZ	PHE- 236	3.5	0	Hydrophobic	false
C12	C6	FAD- 602	4.23	0	Hydrophobic	false
C45	C1'	FAD- 602	4.17	0	Hydrophobic	false