scPDB - 4m6q entry

Protein Data Bank Entry:

PDB ID : 4m6q

Resolution :2.410 Å

Experimental Method : X-ray

Deposition Date : 2013-08-10

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	85 %
B	15 %

Ligand binding site composition:

B-Factor:	16.687
Number of residues:	57
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.792	1420.875

% Hydrophobic	% Polar
38.72	61.28
According to VolSite

Ligand :

HET Code:	20T
Formula:	C26H22F3N4O10PS
Molecular weight:	670.508 g/mol
DrugBank ID:	-
Buried Surface Area:	63.48 %
Polar Surface area:	234.24 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
14.0356	8.10564	3.92147

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	3.94	0	Aromatic Face/Face	false
DuAr	DuAr	TYR- 18	3.94	0	Aromatic Face/Face	false
F47	CG	TYR- 188	4	0	Hydrophobic	false
F49	CD1	TYR- 188	3.65	0	Hydrophobic	false
C15	CB	HIS- 191	4.02	0	Hydrophobic	false
C22	CB	PHE- 193	4.06	0	Hydrophobic	false
C38	CB	PHE- 193	4.39	0	Hydrophobic	false
C33	CD2	PHE- 193	4	0	Hydrophobic	false
DuAr	DuAr	PHE- 193	3.54	0	Aromatic Face/Face	false
N17	OD2	ASP- 219	3.03	157.17	H-Bond (Ligand Donor)	false
F48	CB	TYR- 240	3.85	0	Hydrophobic	false
C2	CG1	VAL- 242	3.55	0	Hydrophobic	false
C5	CG2	VAL- 242	4.31	0	Hydrophobic	false
F48	CG1	VAL- 242	3.32	0	Hydrophobic	false
C12	CG2	VAL- 242	3.45	0	Hydrophobic	false
C12	CB	ALA- 244	3.98	0	Hydrophobic	false
C1	CB	PRO- 273	4.32	0	Hydrophobic	false
C12	CB	SER- 275	3.65	0	Hydrophobic	false
C11	CD1	ILE- 309	4.19	0	Hydrophobic	false
C6	CD1	ILE- 309	3.49	0	Hydrophobic	false
C10	CD1	ILE- 351	3.8	0	Hydrophobic	false
O41	N	GLY- 384	3.43	143.82	H-Bond (Protein Donor)	false
O42	N	GLY- 384	2.62	146.94	H-Bond (Protein Donor)	false