Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

4h5d

2.020 Å

X-ray

2012-09-18

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
F100 %


Ligand binding site composition:

B-Factor:29.762
Number of residues:43
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 3
Water Molecules: 7
Cofactors:
Metals: MG MG MG

Cavity properties

LigandabilityVolume (Å3)
0.278381.375

% Hydrophobic% Polar
44.2555.75
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4h5dHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4h5d_1 Structure
HET Code: YS4
Formula: C15H16N2O7P2
Molecular weight: 398.244 g/mol
DrugBank ID: -
Buried Surface Area:70.79 %
Polar Surface area: 180.15 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 1
Rings: 2
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
16.240730.1813-7.16477
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4h5dRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
C3CZPHE- 983.790Hydrophobic
C2CD1PHE- 994.190Hydrophobic
C4CD1PHE- 993.490Hydrophobic
C8CBPHE- 993.380Hydrophobic
C11CD2LEU- 1004.380Hydrophobic
C1CBALA- 1023.760Hydrophobic
N1OD1ASP- 1033.12120.35H-Bond
(Ligand Donor)
C11CBASP- 1033.760Hydrophobic
C8CBASP- 1033.470Hydrophobic
C1SDMET- 1063.930Hydrophobic
O5CZARG- 1123.780Ionic
(Protein Cationic)
O6CZARG- 1123.140Ionic
(Protein Cationic)
O5NH2ARG- 1122.82140.85H-Bond
(Protein Donor)
O6NH1ARG- 1122.52155.41H-Bond
(Protein Donor)
O6NH2ARG- 1122.91132.74H-Bond
(Protein Donor)
C15CG2THR- 1674.350Hydrophobic
C6CG2THR- 1673.370Hydrophobic
C3CGGLU- 1683.80Hydrophobic
C4CGGLN- 1714.010Hydrophobic
C5CBGLN- 1713.420Hydrophobic
O2NZLYS- 2002.6150.28H-Bond
(Protein Donor)
O2NZLYS- 2002.60Ionic
(Protein Cationic)
O4NZLYS- 2003.790Ionic
(Protein Cationic)
C15CBLYS- 2004.320Hydrophobic
O6NZLYS- 2573.12121.17H-Bond
(Protein Donor)
O7NZLYS- 2572.86160.24H-Bond
(Protein Donor)
O6NZLYS- 2573.120Ionic
(Protein Cationic)
O7NZLYS- 2572.860Ionic
(Protein Cationic)
O3MG MG- 4032.110Metal Acceptor
O5MG MG- 4042.330Metal Acceptor
O3MG MG- 4042.050Metal Acceptor
O7MG MG- 4051.950Metal Acceptor
O4MG MG- 4052.020Metal Acceptor