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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:

3utd

1.700 Å

X-ray

2011-11-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:4-hydroxy-3-methylbut-2-enyl diphosphate reductase
ID:ISPH_ECOLI
AC:P62623
Organism:Escherichia coli
Reign:Bacteria
TaxID:83333
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:15.366
Number of residues:31
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.882266.625

% Hydrophobic% Polar
51.9048.10
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3utdHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80204060Highcharts.com
Ligand :
3utd_2 Structure
HET Code: 0CJ
Formula: C5H9O8P2
Molecular weight: 259.068 g/mol
DrugBank ID: -
Buried Surface Area:80.51 %
Polar Surface area: 158.47 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 0
Rings: 0
Aromatic rings: 0
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-38.4052-0.36506715.8377
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3utdRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


Binding mode :
What is Poseview ?
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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
C28CG2VAL- 153.320Hydrophobic
O15NHIS- 412.76176.29H-Bond
(Protein Donor)
O19ND1HIS- 412.83163.12H-Bond
(Protein Donor)
C27CBALA- 734.260Hydrophobic
O15NE2HIS- 742.91151.68H-Bond
(Protein Donor)
O16NE2HIS- 743.3123.98H-Bond
(Protein Donor)
C22CBCYS- 964.450Hydrophobic
C22CG2VAL- 993.420Hydrophobic
O19NE2HIS- 1242.93167.14H-Bond
(Protein Donor)
C30CG2THR- 1683.560Hydrophobic
O18OG1THR- 1682.84158.92H-Bond
(Protein Donor)
O14OGSER- 2252.64145.14H-Bond
(Protein Donor)
O19NSER- 2262.63156.7H-Bond
(Protein Donor)
O20NASN- 2272.72167.26H-Bond
(Protein Donor)
O20ND2ASN- 2272.83154.78H-Bond
(Protein Donor)
C28CBSER- 2694.30Hydrophobic
O14OGSER- 2692.72156.93H-Bond
(Protein Donor)