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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:

4h4d

1.350 Å

X-ray

2012-09-17

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:11.796
Number of residues:36
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.748405.000

% Hydrophobic% Polar
44.1755.83
According to VolSite

Ligand :
4h4d_2 Structure
HET Code: 10E
Formula: C5H11NO7P2
Molecular weight: 259.091 g/mol
DrugBank ID: -
Buried Surface Area:78.43 %
Polar Surface area: 169.04 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 0
Aromatic rings: 0
Anionic atoms: 3
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-38.9845-0.63466715.6824


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
C6CG2VAL- 153.480Hydrophobic
O13ND1HIS- 412.79159.32H-Bond
(Protein Donor)
O9NHIS- 412.82168.95H-Bond
(Protein Donor)
C4CBALA- 733.380Hydrophobic
O11NE2HIS- 743.3127.33H-Bond
(Protein Donor)
O9NE2HIS- 742.99154.18H-Bond
(Protein Donor)
C1CG2VAL- 994.350Hydrophobic
O13NE2HIS- 1242.8167.46H-Bond
(Protein Donor)
N2OE2GLU- 1263.46125.02H-Bond
(Ligand Donor)
N2OG1THR- 1672.92165.64H-Bond
(Ligand Donor)
C1CG2THR- 1684.190Hydrophobic
O10OGSER- 2252.63159.01H-Bond
(Protein Donor)
O13NSER- 2262.84160.47H-Bond
(Protein Donor)
O15NASN- 2272.75165.64H-Bond
(Protein Donor)
O15ND2ASN- 2272.82160.76H-Bond
(Protein Donor)
C6CBALA- 2684.390Hydrophobic
O10OGSER- 2692.73158.8H-Bond
(Protein Donor)
O14OHOH- 7602.57179.97H-Bond
(Protein Donor)