Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
Protein Data Bank Entry:

1ivh

2.600 Å

X-ray

1997-05-15

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Isovaleryl-CoA dehydrogenase, mitochondrial
ID:IVD_HUMAN
AC:P26440
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:1.3.8.4


Chains:

Chain Name:Percentage of Residues
within binding site
A3 %
B97 %


Ligand binding site composition:

B-Factor:10.091
Number of residues:41
Including
Standard Amino Acids: 37
Non Standard Amino Acids: 1
Water Molecules: 3
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.816448.875

% Hydrophobic% Polar
60.1539.85
According to VolSite

Ligand :
1ivh_2 Structure
HET Code: COS
Formula: C21H32N7O16P3S2
Molecular weight: 795.567 g/mol
DrugBank ID: DB04036
Buried Surface Area:52.6 %
Polar Surface area: 451.41 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 6
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 19

Mass center Coordinates

XYZ
16.171868.4465-45.6586


Binding mode :
What is Poseview ?
  • 2D View
  • 3D View
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
S1PCD1LEU- 1034.370Hydrophobic
C2PSDMET- 1353.970Hydrophobic
OAPOSER- 1423.11163.53H-Bond
(Ligand Donor)
N8POSER- 1422.75160.91H-Bond
(Ligand Donor)
CAPCG1VAL- 1444.360Hydrophobic
C6PCBVAL- 1444.140Hydrophobic
O7AOGSER- 1903.19150.32H-Bond
(Protein Donor)
C4BCBSER- 1903.790Hydrophobic
C4BCG2VAL- 2443.480Hydrophobic
C1BCGMET- 2483.80Hydrophobic
CAPCEMET- 2484.330Hydrophobic
C5BCEMET- 2483.980Hydrophobic
C6PCD2LEU- 2514.150Hydrophobic
N6AOD2ASP- 2523.33150.02H-Bond
(Ligand Donor)
CDPCZPHE- 2833.290Hydrophobic
CEPCG1VAL- 3803.620Hydrophobic
CEPCG2VAL- 3843.960Hydrophobic
S'PC2'FAD- 3993.510Hydrophobic
O4AOHOH- 5452.81162.84H-Bond
(Protein Donor)