scPDB - 2h3d entry

Protein Data Bank Entry:

PDB ID : 2h3d

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-05-22

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_MOUSE
AC:	Q99KQ4
Organism:	Mus musculus
Reign:	Eukaryota
TaxID:	10090
EC Number:	2.4.2.12

Chains:

Chain Name:	Percentage of Residues within binding site
A	16 %
B	84 %

Ligand binding site composition:

B-Factor:	28.788
Number of residues:	41
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.426	1174.500

% Hydrophobic	% Polar
29.89	70.11
According to VolSite

Ligand :

HET Code:	NMN
Formula:	C11H14N2O8P
Molecular weight:	333.211 g/mol
DrugBank ID:	DB03227
Buried Surface Area:	61.5 %
Polar Surface area:	178.89 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
13.2848	7.38727	32.7685

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
C5	CB	ASP- 16	4.26	0	Hydrophobic	false
C4	CE2	TYR- 18	3.44	0	Hydrophobic	false
C2R	CD2	PHE- 193	3.64	0	Hydrophobic	false
C5	CB	PHE- 193	3.76	0	Hydrophobic	false
DuAr	DuAr	PHE- 193	3.83	0	Aromatic Face/Face	false
C5R	CD	ARG- 196	4.39	0	Hydrophobic	false
N7	OD2	ASP- 219	3.17	172.94	H-Bond (Ligand Donor)	false
C4	CB	ASP- 219	4.07	0	Hydrophobic	false
O3R	OD1	ASP- 313	2.79	144.68	H-Bond (Ligand Donor)	false
O3P	N	GLY- 384	2.81	152.67	H-Bond (Protein Donor)	false
O2P	N	GLY- 384	3.43	143.05	H-Bond (Protein Donor)	false