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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:

2jcv

2.200 Å

X-ray

2007-01-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:1-deoxy-D-xylulose 5-phosphate reductoisomerase
ID:DXR_MYCTU
AC:P9WNS1
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B100 %


Ligand binding site composition:

B-Factor:14.494
Number of residues:47
Including
Standard Amino Acids: 45
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2301123.875

% Hydrophobic% Polar
36.0463.96
According to VolSite

Ligand :
2jcv_1 Structure
HET Code: NDP
Formula: C21H26N7O17P3
Molecular weight: 741.389 g/mol
DrugBank ID: DB02338
Buried Surface Area:55.46 %
Polar Surface area: 404.9 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 5
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
11.1571-4.5950290.7589


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
O3BNTHR- 213.22129.02H-Bond
(Protein Donor)
O1XOG1THR- 212.91137.47H-Bond
(Protein Donor)
O3BOG1THR- 212.7163.66H-Bond
(Ligand Donor)
O2ANSER- 233.02164.47H-Bond
(Protein Donor)
O2NNILE- 243.01154.03H-Bond
(Protein Donor)
C5DCG1ILE- 244.370Hydrophobic
C4NCD1ILE- 244.40Hydrophobic
O2BNGLY- 472.81160.76H-Bond
(Protein Donor)
O2XNGLY- 483.04149.23H-Bond
(Protein Donor)
O2XNHIS- 502.8164.5H-Bond
(Protein Donor)
C1BCD2LEU- 1043.970Hydrophobic
C5BCG1VAL- 1053.840Hydrophobic
C4DCBALA- 1264.010Hydrophobic
C1DCBALA- 1264.310Hydrophobic
O3DNLYS- 1283.05160.93H-Bond
(Protein Donor)
C1DCGLYS- 1284.150Hydrophobic
C4NCEMET- 2674.180Hydrophobic
O2NOHOH- 22632.54155.3H-Bond
(Protein Donor)
O7NOHOH- 22642.73163.02H-Bond
(Protein Donor)