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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:

1i12

1.300 Å

X-ray

2001-01-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glucosamine 6-phosphate N-acetyltransferase
ID:GNA1_YEAST
AC:P43577
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:559292
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:15.055
Number of residues:40
Including
Standard Amino Acids: 36
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors: ACO
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.9081481.625

% Hydrophobic% Polar
28.4771.53
According to VolSite

Ligand :
1i12_3 Structure
HET Code: ACO
Formula: C23H34N7O17P3S
Molecular weight: 805.539 g/mol
DrugBank ID: -
Buried Surface Area:51.32 %
Polar Surface area: 429.68 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 20

Mass center Coordinates

XYZ
93.4026-2.9096751.8186


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
C6PCG2VAL- 263.810Hydrophobic
C6PCD1LEU- 274.070Hydrophobic
C2PCD1LEU- 273.40Hydrophobic
CEPCG2ILE- 1003.720Hydrophobic
C2PCBILE- 1004.410Hydrophobic
CH3CG1ILE- 1003.950Hydrophobic
N4POILE- 1002.9142.22H-Bond
(Ligand Donor)
ONILE- 1003.08168.53H-Bond
(Protein Donor)
CEPCG2VAL- 1024.050Hydrophobic
CAPCBVAL- 1024.130Hydrophobic
O9PNVAL- 1022.86160.04H-Bond
(Protein Donor)
CAPCGGLN- 1074.020Hydrophobic
O4ANGLY- 1083.07155.76H-Bond
(Protein Donor)
O1ANGLY- 1102.8149.28H-Bond
(Protein Donor)
O5ANGLY- 1122.93146.89H-Bond
(Protein Donor)
C5BCBLYS- 1133.820Hydrophobic
O2ANLYS- 1132.89160.36H-Bond
(Protein Donor)
CH3CBLEU- 1334.010Hydrophobic
S1PCBCYS- 1353.790Hydrophobic
O5PND2ASN- 1393.28155.48H-Bond
(Protein Donor)
O2BNZLYS- 1412.82175.43H-Bond
(Protein Donor)
O7ANZLYS- 1413.590Ionic
(Protein Cationic)
CCPCE1PHE- 1423.610Hydrophobic
CDPCD2PHE- 1424.180Hydrophobic
C5BCD1PHE- 1423.750Hydrophobic
CEPCE2PHE- 1424.020Hydrophobic
S1PCE2TYR- 1433.910Hydrophobic
CH3CZTYR- 1434.460Hydrophobic
C1BCGLYS- 1454.160Hydrophobic
C4BCBLYS- 1453.90Hydrophobic
O8ANZLYS- 1452.9160.14H-Bond
(Protein Donor)
O8ANZLYS- 1452.90Ionic
(Protein Cationic)
O5AOHOH- 12022.62153.49H-Bond
(Protein Donor)