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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:

4kqs

1.970 Å

X-ray

2013-05-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Farnesyl pyrophosphate synthase
ID:FPPS_HUMAN
AC:P14324
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.5.1.10


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:30.931
Number of residues:25
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 2
Water Molecules: 3
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.253742.500

% Hydrophobic% Polar
40.4559.55
According to VolSite

Ligand :
4kqs_1 Structure
HET Code: IPE
Formula: C5H9O7P2
Molecular weight: 243.068 g/mol
DrugBank ID: DB04714
Buried Surface Area:61.61 %
Polar Surface area: 141.4 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 0
Rings: 0
Aromatic rings: 0
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
34.2009-8.9257911.6188


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
O1ANZLYS- 573.710Ionic
(Protein Cationic)
O2ANZLYS- 572.770Ionic
(Protein Cationic)
O1BNZLYS- 573.150Ionic
(Protein Cationic)
O2ANZLYS- 572.77176.45H-Bond
(Protein Donor)
O1BNZLYS- 573.15120.14H-Bond
(Protein Donor)
O1BNLYS- 572.97170.84H-Bond
(Protein Donor)
O1NH2ARG- 602.93144.57H-Bond
(Protein Donor)
O1ANH2ARG- 603.31125.52H-Bond
(Protein Donor)
O1ANH1ARG- 602.55163.93H-Bond
(Protein Donor)
O1ACZARG- 603.350Ionic
(Protein Cationic)
O1NE2GLN- 962.87144.73H-Bond
(Protein Donor)
O3BNE2GLN- 962.91168.82H-Bond
(Protein Donor)
C2CD2LEU- 1004.180Hydrophobic
O2BNH2ARG- 1133.35131.85H-Bond
(Protein Donor)
O2BNEARG- 1132.82158.44H-Bond
(Protein Donor)
O3BNH2ARG- 1132.76151.18H-Bond
(Protein Donor)
O2BCZARG- 1133.510Ionic
(Protein Cationic)
O3BCZARG- 1133.770Ionic
(Protein Cationic)
C4CG2THR- 2013.730Hydrophobic
C4CBSER- 2054.380Hydrophobic
C5CE2PHE- 2393.610Hydrophobic
C5CBASP- 24340Hydrophobic
O3BOHOH- 5152.92179.98H-Bond
(Protein Donor)