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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:

2ncd

2.500 Å

X-ray

1999-06-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Protein claret segregational
ID:NCD_DROME
AC:P20480
Organism:Drosophila melanogaster
Reign:Eukaryota
TaxID:7227
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:13.292
Number of residues:30
Including
Standard Amino Acids: 30
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.182256.500

% Hydrophobic% Polar
64.4735.53
According to VolSite

Ligand :
2ncd_1 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:51.74 %
Polar Surface area: 260.7 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 6

Mass center Coordinates

XYZ
6.1944853.454243.9998


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
C1'CD2LEU- 3593.820Hydrophobic
O1BNGLY- 4372.6153.75H-Bond
(Protein Donor)
O2BOGSER- 4383.21153.43H-Bond
(Protein Donor)
O2BNSER- 4382.76128.92H-Bond
(Protein Donor)
O2BNGLY- 4393.34162.8H-Bond
(Protein Donor)
O1BNZLYS- 4403.680Ionic
(Protein Cationic)
O2BNZLYS- 4402.950Ionic
(Protein Cationic)
O2BNZLYS- 4402.95128.65H-Bond
(Protein Donor)
O2ANTYR- 4423169.54H-Bond
(Protein Donor)
C5'CBTYR- 4423.670Hydrophobic
C2'CD2TYR- 4423.70Hydrophobic
DuArDuArTYR- 4423.750Aromatic Face/Face