scPDB - 4jr5 entry

Protein Data Bank Entry:

PDB ID : 4jr5

Resolution :1.910 Å

Experimental Method : X-ray

Deposition Date : 2013-03-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nicotinamide phosphoribosyltransferase
ID:	NAMPT_HUMAN
AC:	P43490
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.4.2.12

Chains:

Chain Name:	Percentage of Residues within binding site
A	91 %
B	9 %

Ligand binding site composition:

B-Factor:	8.126
Number of residues:	37
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.958	1404.000

% Hydrophobic	% Polar
41.59	58.41
According to VolSite

Ligand :

HET Code:	1LS
Formula:	C18H22N4O2S2
Molecular weight:	390.523 g/mol
DrugBank ID:	-
Buried Surface Area:	62.49 %
Polar Surface area:	114.8 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
14.7835	7.55154	0.370846

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
C1	CB	ASP- 16	4.19	0	Hydrophobic	false
C2	CB	TYR- 18	4.46	0	Hydrophobic	false
DuAr	DuAr	TYR- 18	3.82	0	Aromatic Face/Face	false
C25	CB	TYR- 188	4.34	0	Hydrophobic	false
C17	CB	HIS- 191	4.07	0	Hydrophobic	false
C1	CB	PHE- 193	4.34	0	Hydrophobic	false
S10	CZ	PHE- 193	3.48	0	Hydrophobic	false
DuAr	DuAr	PHE- 193	3.73	0	Aromatic Face/Face	false
C1	CB	ASP- 219	3.87	0	Hydrophobic	false
C24	CG1	VAL- 242	4.2	0	Hydrophobic	false
C13	CG2	VAL- 242	3.52	0	Hydrophobic	false
S10	CB	ALA- 244	4.38	0	Hydrophobic	false
C24	CG	PRO- 273	4.05	0	Hydrophobic	false
C23	CB	PRO- 273	4.23	0	Hydrophobic	false
S10	CB	SER- 275	3.75	0	Hydrophobic	false
C13	CB	SER- 275	3.42	0	Hydrophobic	false
C22	CD1	ILE- 309	3.69	0	Hydrophobic	false
C14	CD1	ILE- 309	4.09	0	Hydrophobic	false
S10	CD	ARG- 311	3.75	0	Hydrophobic	false
S10	CG2	ILE- 351	3.81	0	Hydrophobic	false
C16	CD1	ILE- 351	3.61	0	Hydrophobic	false
N11	O	HOH- 732	2.87	146.97	H-Bond (Ligand Donor)	false