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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4kfp

1.840 Å

X-ray

2013-04-27

Interactomes:
Molecular Function:
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
A9 %
B91 %


Ligand binding site composition:

B-Factor:11.660
Number of residues:46
Including
Standard Amino Acids: 43
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9871346.625

% Hydrophobic% Polar
41.6058.40
According to VolSite

Ligand :
4kfp_2 Structure
HET Code: 1R7
Formula: C25H31N4O4S
Molecular weight: 483.603 g/mol
DrugBank ID: -
Buried Surface Area:61.32 %
Polar Surface area: 103.11 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
9.65191-5.6663245.1113


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C28CBTYR- 1884.340Hydrophobic
C4CBHIS- 1914.380Hydrophobic
DuArDuArPHE- 1933.970Aromatic Face/Face
C14CBPHE- 1933.640Hydrophobic
N8OD2ASP- 2193.23146.65H-Bond
(Ligand Donor)
N8OD1ASP- 2193.4141.02H-Bond
(Ligand Donor)
C24CG2VAL- 2424.170Hydrophobic
C6CG2VAL- 2423.650Hydrophobic
C1CBALA- 2444.350Hydrophobic
C30CGPRO- 2734.270Hydrophobic
C34CGPRO- 2734.330Hydrophobic
C1CBSER- 2753.520Hydrophobic
C30CGPRO- 3073.840Hydrophobic
C24CD1ILE- 3093.740Hydrophobic
C3CD1ILE- 3513.770Hydrophobic
C2CD1ILE- 3513.770Hydrophobic