scPDB - 4lva entry

Protein Data Bank Entry:

PDB ID : 4lva

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2013-07-26

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	88 %
B	12 %

Ligand binding site composition:

B-Factor:	11.287
Number of residues:	45
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.765	1255.500

% Hydrophobic	% Polar
37.90	62.10
According to VolSite

Ligand :

HET Code:	20M
Formula:	C22H29N6O4S2
Molecular weight:	505.633 g/mol
DrugBank ID:	-
Buried Surface Area:	60.57 %
Polar Surface area:	142.02 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
15.3846	5.30385	-0.109706

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
DuAr	DuAr	TYR- 18	3.97	0	Aromatic Face/Face	false
C32	CE2	TYR- 188	3.57	0	Hydrophobic	false
C33	CD2	TYR- 188	3.88	0	Hydrophobic	false
C28	CB	TYR- 188	3.67	0	Hydrophobic	false
C4	CB	HIS- 191	4.05	0	Hydrophobic	false
C12	CB	PHE- 193	4.1	0	Hydrophobic	false
DuAr	DuAr	PHE- 193	3.52	0	Aromatic Face/Face	false
N8	OD1	ASP- 219	3.09	155.65	H-Bond (Ligand Donor)	false
N8	OD2	ASP- 219	3.32	129.14	H-Bond (Ligand Donor)	false
N10	OD2	ASP- 219	2.74	175.73	H-Bond (Ligand Donor)	false
C7	CG2	VAL- 242	4.01	0	Hydrophobic	false
C26	CG1	VAL- 242	4.38	0	Hydrophobic	false
C1	CG2	VAL- 242	3.36	0	Hydrophobic	false
C1	CB	ALA- 244	4.43	0	Hydrophobic	false
C7	CB	ALA- 244	3.57	0	Hydrophobic	false
C26	CB	PRO- 273	4.19	0	Hydrophobic	false
C1	CB	SER- 275	3.57	0	Hydrophobic	false
C2	CD1	ILE- 309	3.87	0	Hydrophobic	false
C25	CD1	ILE- 309	3.56	0	Hydrophobic	false
O19	NH2	ARG- 311	3.29	120.9	H-Bond (Protein Donor)	false
C3	CD1	ILE- 351	3.55	0	Hydrophobic	false