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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:

4kuh

2.510 Å

X-ray

2013-05-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-hydroxybutyryl-CoA dehydrogenase
ID:C4IEM5_CLOBU
AC:C4IEM5
Organism:Clostridium butyricum E4 str. BoNT E BL5262
Reign:Bacteria
TaxID:632245
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A90 %
B10 %


Ligand binding site composition:

B-Factor:53.519
Number of residues:31
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.576945.000

% Hydrophobic% Polar
54.6445.36
According to VolSite

Ligand :
4kuh_1 Structure
HET Code: CAA
Formula: C25H36N7O18P3S
Molecular weight: 847.576 g/mol
DrugBank ID: DB03059
Buried Surface Area:37.13 %
Polar Surface area: 446.75 Å2
Number of
H-Bond Acceptors: 23
H-Bond Donors: 5
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 22

Mass center Coordinates

XYZ
21.406856.7203-19.6211


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
C4CGMET- 124.360Hydrophobic
DuArNZLYS- 503.85143.48Pi/Cation
C2BCD2LEU- 514.480Hydrophobic
O8ANZLYS- 563.23152.52H-Bond
(Protein Donor)
O8ANZLYS- 563.230Ionic
(Protein Cationic)
C4CBSER- 1174.350Hydrophobic
O3NE2HIS- 1382.68164.22H-Bond
(Protein Donor)
C2PCD2PHE- 1403.680Hydrophobic
N4POASN- 1413.14140.86H-Bond
(Ligand Donor)
C4BCG2VAL- 1453.880Hydrophobic
C6PCEMET- 1464.070Hydrophobic
CAPCBASN- 2214.410Hydrophobic
OAPOD1ASN- 2213.4126.71H-Bond
(Ligand Donor)
CEPCEMET- 2243.450Hydrophobic
C6PCD1LEU- 2294.450Hydrophobic
CDPCD2LEU- 2324.350Hydrophobic
S1PCD1ILE- 2334.240Hydrophobic
C2CG1VAL- 2374.280Hydrophobic
C2CD1ILE- 2414.40Hydrophobic