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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:

1wze

2.000 Å

X-ray

2005-03-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Malate dehydrogenase
ID:MDH_THETH
AC:P10584
Organism:Thermus thermophilus
Reign:Bacteria
TaxID:274
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:13.964
Number of residues:35
Including
Standard Amino Acids: 31
Non Standard Amino Acids: 0
Water Molecules: 4
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.703587.250

% Hydrophobic% Polar
29.8970.11
According to VolSite

Ligand :
1wze_1 Structure
HET Code: NAD
Formula: C21H26N7O14P2
Molecular weight: 662.417 g/mol
DrugBank ID: -
Buried Surface Area:48.46 %
Polar Surface area: 343.54 Å2
Number of
H-Bond Acceptors: 18
H-Bond Donors: 6
Rings: 5
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 11

Mass center Coordinates

XYZ
23.280926.698325.1585


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
O2ANGLN- 142.89172.28H-Bond
(Protein Donor)
O2NNILE- 152.94171.46H-Bond
(Protein Donor)
C5NCD1ILE- 153.930Hydrophobic
C5DCD1ILE- 153.720Hydrophobic
C5DCG1VAL- 863.930Hydrophobic
C3NCG1VAL- 1284.070Hydrophobic
N7NOVAL- 1283.33169.82H-Bond
(Ligand Donor)
O3DNASN- 1303.04153.44H-Bond
(Protein Donor)
O2DND2ASN- 1302.92152.17H-Bond
(Protein Donor)
C3NCEMET- 1544.260Hydrophobic
N7NOMET- 1543.32174.05H-Bond
(Ligand Donor)
C4NCD2LEU- 1573.740Hydrophobic
O1NOGSER- 2403.24129.77H-Bond
(Protein Donor)
C4NCBALA- 2453.680Hydrophobic
O2NOHOH- 13523.15142.1H-Bond
(Protein Donor)
O7NOHOH- 13822.71159.57H-Bond
(Protein Donor)