Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1ml3

2.500 Å

X-ray

2002-08-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
ID:G3PG_TRYCR
AC:P22513
Organism:Trypanosoma cruzi
Reign:Eukaryota
TaxID:5693
EC Number:1.2.1.12


Chains:

Chain Name:Percentage of Residues
within binding site
B9 %
C91 %


Ligand binding site composition:

B-Factor:46.054
Number of residues:45
Including
Standard Amino Acids: 43
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.4941100.250

% Hydrophobic% Polar
48.7751.23
According to VolSite

Ligand :
1ml3_2 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:55.31 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
3.718052.9467747.3456


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
O2ANARG- 123.28162.73H-Bond
(Protein Donor)
O1NNILE- 133.02166.38H-Bond
(Protein Donor)
C4NCD1ILE- 133.480Hydrophobic
C1BCGMET- 394.10Hydrophobic
N6AOGLN- 913.42164.49H-Bond
(Ligand Donor)
C2DCBALA- 1354.390Hydrophobic
C4NSGCYS- 1663.510Hydrophobic
O7NND2ASN- 3353.27173.9H-Bond
(Protein Donor)
C5NCBTYR- 3394.20Hydrophobic