scPDB - 1yb5 entry

Protein Data Bank Entry:

PDB ID : 1yb5

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2004-12-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Quinone oxidoreductase
ID:	QOR_HUMAN
AC:	Q08257
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.6.5.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	96 %

Ligand binding site composition:

B-Factor:	26.900
Number of residues:	57
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
1.294	1390.500

% Hydrophobic	% Polar
46.84	53.16
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	63.64 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
7.92731	-28.0655	28.8452

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
C2D	CB	PRO- 49	3.91	0	Hydrophobic	false
O3D	OH	TYR- 53	3.01	128.31	H-Bond (Protein Donor)	false
O2D	OH	TYR- 53	2.71	130.6	H-Bond (Protein Donor)	false
C5N	CG2	ILE- 131	3.39	0	Hydrophobic	false
C4N	CG2	THR- 135	3.39	0	Hydrophobic	false
O3B	OG	SER- 158	2.77	172.72	H-Bond (Ligand Donor)	false
O3B	N	SER- 158	3.23	124.23	H-Bond (Protein Donor)	false
O1X	OG	SER- 158	2.72	155.43	H-Bond (Protein Donor)	false
O2A	N	GLY- 160	2.93	166	H-Bond (Protein Donor)	false
O1N	N	VAL- 161	2.87	157.18	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 161	4.44	0	Hydrophobic	false
C5N	CG2	VAL- 161	3.77	0	Hydrophobic	false
O1X	N	GLY- 181	2.74	154.58	H-Bond (Protein Donor)	false
O2X	NE2	HIS- 200	2.79	163.31	H-Bond (Protein Donor)	false
DuAr	DuAr	HIS- 200	3.64	0	Aromatic Face/Face	false
C5D	SD	MET- 224	4.02	0	Hydrophobic	false
C4D	CB	MET- 224	4.25	0	Hydrophobic	false
N1A	ND2	ASN- 229	2.93	167.7	H-Bond (Protein Donor)	false
C3N	CG1	VAL- 246	4.07	0	Hydrophobic	false
N7N	O	VAL- 246	2.94	168.46	H-Bond (Ligand Donor)	false
O3D	NH1	ARG- 249	3.39	122.2	H-Bond (Protein Donor)	false
N7N	O	VAL- 269	2.74	158.95	H-Bond (Ligand Donor)	false
O7N	N	LEU- 271	2.88	167.34	H-Bond (Protein Donor)	false
C3B	CB	ALA- 321	4.28	0	Hydrophobic	false
O3X	N	ALA- 321	2.76	168.97	H-Bond (Protein Donor)	false
O1A	O	HOH- 867	2.6	156.77	H-Bond (Protein Donor)	false
N6A	O	HOH- 944	2.93	157.06	H-Bond (Ligand Donor)	false