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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:

2o07

1.890 Å

X-ray

2006-11-27

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Spermidine synthase
ID:SPEE_HUMAN
AC:P19623
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:2.5.1.16


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:21.908
Number of residues:28
Including
Standard Amino Acids: 27
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.959702.000

% Hydrophobic% Polar
49.0450.96
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2o07HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2o07_1 Structure
HET Code: MTA
Formula: C11H15N5O3S
Molecular weight: 297.333 g/mol
DrugBank ID: DB02282
Buried Surface Area:71.37 %
Polar Surface area: 144.61 Å2
Number of
H-Bond Acceptors: 8
H-Bond Donors: 3
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 3

Mass center Coordinates

XYZ
2.95266.71667.44965
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2o07RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80510Highcharts.com


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'NE2GLN- 492.9163.19H-Bond
(Protein Donor)
CSCD2LEU- 634.170Hydrophobic
CSCD1LEU- 653.90Hydrophobic
C3'CD1LEU- 653.70Hydrophobic
CSCBGLN- 704.130Hydrophobic
O2'OE2GLU- 1242.69164.05H-Bond
(Ligand Donor)
O3'OE1GLU- 1242.57161.16H-Bond
(Ligand Donor)
O3'OE2GLU- 1243.23133.5H-Bond
(Ligand Donor)
C1'CG2ILE- 1254.360Hydrophobic
N3NILE- 1253.43146.32H-Bond
(Protein Donor)
CSCG1VAL- 1294.420Hydrophobic
C3'CG1VAL- 1294.410Hydrophobic
N6OD1ASP- 1552.78164.7H-Bond
(Ligand Donor)
N1NGLY- 1562.79165.05H-Bond
(Protein Donor)
O4'NSER- 1753.41133.82H-Bond
(Protein Donor)
C5'CBSER- 1754.070Hydrophobic
C2'CBSER- 1753.910Hydrophobic