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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:

1kh2

2.300 Å

X-ray

2001-11-29

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Argininosuccinate synthase
ID:ASSY_THET8
AC:P59846
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:300852
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
D100 %


Ligand binding site composition:

B-Factor:36.838
Number of residues:34
Including
Standard Amino Acids: 33
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9931258.875

% Hydrophobic% Polar
32.1767.83
According to VolSite

Ligand :
1kh2_4 Structure
HET Code: ATP
Formula: C10H12N5O13P3
Molecular weight: 503.149 g/mol
DrugBank ID: DB00171
Buried Surface Area:57.25 %
Polar Surface area: 319.88 Å2
Number of
H-Bond Acceptors: 17
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
33.169451.715934.2226


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
O2'OALA- 62.62154.62H-Bond
(Ligand Donor)
C2'CBALA- 63.990Hydrophobic
O3GNGLY- 103.13120.54H-Bond
(Protein Donor)
O2GNASP- 122.76128.64H-Bond
(Protein Donor)
O1GNTHR- 133.24126.66H-Bond
(Protein Donor)
C3'CG2THR- 133.70Hydrophobic
N6OALA- 332.99147.54H-Bond
(Ligand Donor)
N1NALA- 333.27167.53H-Bond
(Protein Donor)
O2'NGLY- 1142.9163H-Bond
(Protein Donor)
C4'CE1PHE- 1254.140Hydrophobic
C1'CZPHE- 1253.470Hydrophobic