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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:

3ldp

2.200 Å

X-ray

2010-01-13

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:5.6205.6205.6200.0005.6201

List of CHEMBLId :

CHEMBL1614768


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:78 kDa glucose-regulated protein
ID:GRP78_HUMAN
AC:P11021
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:35.883
Number of residues:32
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.8591366.875

% Hydrophobic% Polar
40.2559.75
According to VolSite

Ligand :
3ldp_1 Structure
HET Code: 3P1
Formula: C20H21N7O4
Molecular weight: 423.425 g/mol
DrugBank ID: -
Buried Surface Area:59.02 %
Polar Surface area: 164.46 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 5
Rings: 5
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 5

Mass center Coordinates

XYZ
17.5221-9.146715.35152


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
C28CE1TYR- 393.530Hydrophobic
C17CD1ILE- 614.230Hydrophobic
C21CD1ILE- 614.20Hydrophobic
O31OE1GLU- 2932.62136.2H-Bond
(Ligand Donor)
O31OE2GLU- 2932.95153.49H-Bond
(Ligand Donor)
O30NZLYS- 2963.49126.1H-Bond
(Protein Donor)
O31NZLYS- 2962.67133.49H-Bond
(Protein Donor)
C24CDARG- 2974.460Hydrophobic
C22CDARG- 2974.20Hydrophobic
DuArCZARG- 2973.363.18Pi/Cation
N1OGSER- 3002.6148.14H-Bond
(Protein Donor)