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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:

4xyl

1.950 Å

X-ray

2015-02-02

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
A100 %


Ligand binding site composition:

B-Factor:29.114
Number of residues:42
Including
Standard Amino Acids: 40
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.684337.500

% Hydrophobic% Polar
60.0040.00
According to VolSite

Ligand :
4xyl_1 Structure
HET Code: COA
Formula: C21H32N7O16P3S
Molecular weight: 763.502 g/mol
DrugBank ID: DB01992
Buried Surface Area:49.38 %
Polar Surface area: 426.11 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 18

Mass center Coordinates

XYZ
35.911211.787485.1147


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
O7AOGSER- 192.52151.19H-Bond
(Protein Donor)
O7ANZLYS- 243.08160.58H-Bond
(Protein Donor)
O2ANZLYS- 242.56165H-Bond
(Protein Donor)
O7ANZLYS- 243.080Ionic
(Protein Cationic)
O2ANZLYS- 242.560Ionic
(Protein Cationic)
C5BCDLYS- 244.350Hydrophobic
CEPCG1ILE- 253.50Hydrophobic
O8AND2ASN- 462.83173.56H-Bond
(Protein Donor)
C1BCGPRO- 474.010Hydrophobic
C1BCG1VAL- 754.440Hydrophobic
CCPCGPRO- 764.340Hydrophobic
C6PCG2ILE- 984.310Hydrophobic
N4POILE- 983.21156.79H-Bond
(Ligand Donor)
CDPCG2THR- 993.960Hydrophobic
O9PNSER- 1002.81177.45H-Bond
(Protein Donor)
C6PCBSER- 1004.170Hydrophobic
C2PCBPHE- 1314.120Hydrophobic
S1PCD2PHE- 1314.20Hydrophobic
C2PCZPHE- 1443.650Hydrophobic
O4AOHOH- 6362.97163.58H-Bond
(Protein Donor)