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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:

4xz3

2.400 Å

X-ray

2015-02-03

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
A95 %
C5 %


Ligand binding site composition:

B-Factor:63.764
Number of residues:43
Including
Standard Amino Acids: 42
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: ACP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.2771211.625

% Hydrophobic% Polar
44.2955.71
According to VolSite

Ligand :
4xz3_1 Structure
HET Code: COA
Formula: C21H32N7O16P3S
Molecular weight: 763.502 g/mol
DrugBank ID: DB01992
Buried Surface Area:50.84 %
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
34.327410.63991.6235


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- 192.58140.12H-Bond
(Protein Donor)
O2ANZLYS- 243.490Ionic
(Protein Cationic)
O5ANZLYS- 243.180Ionic
(Protein Cationic)
O5ANZLYS- 243.18167.13H-Bond
(Protein Donor)
CEPCD1ILE- 253.590Hydrophobic
C6PCD1ILE- 253.620Hydrophobic
O8AND2ASN- 462.75146.37H-Bond
(Protein Donor)
C1BCGPRO- 474.290Hydrophobic
C5BCG1VAL- 754.360Hydrophobic
CCPCGPRO- 764.480Hydrophobic
N4POILE- 983.22137.58H-Bond
(Ligand Donor)
CDPCG2THR- 993.830Hydrophobic
O9PNSER- 1002.85160.99H-Bond
(Protein Donor)
C2PCBPHE- 1313.980Hydrophobic
C2PCZPHE- 1443.570Hydrophobic