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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:

4y8v

2.100 Å

X-ray

2015-02-16

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Acyl-CoA synthetase (NDP forming)
ID:B1L3C9_KORCO
AC:B1L3C9
Organism:Korarchaeum cryptofilum
Reign:Archaea
TaxID:374847
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A34 %
C66 %


Ligand binding site composition:

B-Factor:33.248
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: MG

Cavity properties

LigandabilityVolume (Å3)
0.3832210.625

% Hydrophobic% Polar
46.7253.28
According to VolSite

Ligand :
4y8v_3 Structure
HET Code: ADP
Formula: C10H12N5O10P2
Molecular weight: 424.177 g/mol
DrugBank ID: -
Buried Surface Area:51.53 %
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
91.1679-21.26873.2947


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
O2AND2ASN- 1293.15162.99H-Bond
(Protein Donor)
O2BOGSER- 1602.75158.27H-Bond
(Protein Donor)
O3ANGLY- 1612.99174.26H-Bond
(Protein Donor)
O1BNALA- 1622.91156.4H-Bond
(Protein Donor)
DuArDuArHIS- 2543.810Aromatic Face/Face
O3BNGLY- 3083.3149.89H-Bond
(Protein Donor)
O2BNGLY- 3093.27165.1H-Bond
(Protein Donor)
O3BMG MG- 6012.340Metal Acceptor