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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:

3doc

2.400 Å

X-ray

2008-07-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glyceraldehyde-3-phosphate dehydrogenase
ID:Q2YRE0_BRUA2
AC:Q2YRE0
Organism:Brucella abortus
Reign:Bacteria
TaxID:359391
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A9 %
B91 %


Ligand binding site composition:

B-Factor:21.659
Number of residues:51
Including
Standard Amino Acids: 47
Non Standard Amino Acids: 0
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.1981015.875

% Hydrophobic% Polar
37.8762.13
According to VolSite

Ligand :
3doc_2 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:56.56 %
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
3.8001410.590628.2575


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
O2ANARG- 123.07171.7H-Bond
(Protein Donor)
O2NNILE- 133167.36H-Bond
(Protein Donor)
C5DCG2ILE- 133.420Hydrophobic
O3BOD2ASP- 363.1164.91H-Bond
(Ligand Donor)
O2BOD1ASP- 362.97161.14H-Bond
(Ligand Donor)
N6AOARG- 803.41167.95H-Bond
(Ligand Donor)
O4DOGSER- 1223.19165.18H-Bond
(Protein Donor)
C5NCBCYS- 1533.690Hydrophobic
O7NND2ASN- 3162.73163.45H-Bond
(Protein Donor)
C5NCBPHE- 3204.460Hydrophobic
O2AOHOH- 9922.63169.24H-Bond
(Protein Donor)
O2NOHOH- 10602.59179.98H-Bond
(Protein Donor)