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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:

1m67

2.500 Å

X-ray

2002-07-12

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal
ID:GPDA_LEIME
AC:P90551
Organism:Leishmania mexicana
Reign:Eukaryota
TaxID:5665
EC Number:1.1.1.8


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:47.745
Number of residues:8
Including
Standard Amino Acids: 8
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.048313.875

% Hydrophobic% Polar
68.8231.18
According to VolSite

Ligand :
1m67_1 Structure
HET Code: BOA
Formula: C5H3BrN4O
Molecular weight: 215.008 g/mol
DrugBank ID: DB04283
Buried Surface Area:34.66 %
Polar Surface area: 74.69 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 2
Rings: 2
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 0

Mass center Coordinates

XYZ
34.222454.765430.1223


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
BRCZ3TRP- 443.930Hydrophobic
BRCG2ILE- 933.890Hydrophobic
BRCBPHE- 973.890Hydrophobic
DuArDuArPHE- 973.540Aromatic Face/Face
BRCBPHE- 1014.270Hydrophobic