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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:

1y7l

1.550 Å

X-ray

2004-12-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Cysteine synthase
ID:CYSK_HAEIN
AC:P45040
Organism:Haemophilus influenzae
Reign:Bacteria
TaxID:71421
EC Number:2.5.1.47


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:16.956
Number of residues:35
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 1
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.889695.250

% Hydrophobic% Polar
39.3260.68
According to VolSite

Ligand :
1y7l_1 Structure
HET Code: ASN_LEU_ASN_ILE
Formula: C20H36N6O7
Molecular weight: 472.536 g/mol
DrugBank ID: -
Buried Surface Area:53.41 %
Polar Surface area: 241.24 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 6
Rings: 0
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 15

Mass center Coordinates

XYZ
19.60211.5071541.5862


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
OXTOG1THR- 692.73164.98H-Bond
(Protein Donor)
OD1NSER- 702.99169.76H-Bond
(Protein Donor)
ND2OGSER- 703.06163.11H-Bond
(Ligand Donor)
ONTHR- 733.04163.87H-Bond
(Protein Donor)
CBSDMET- 1203.780Hydrophobic
CD1CD1ILE- 1244.210Hydrophobic
OXTNE2GLN- 1432.79176.34H-Bond
(Protein Donor)
CBCZPHE- 1444.360Hydrophobic
CD1CZPHE- 1443.970Hydrophobic
CD2CBALA- 2314.420Hydrophobic
CD1CBALA- 2314.080Hydrophobic
CD2CE2PHE- 2333.50Hydrophobic