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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:

1nbu

1.600 Å

X-ray

2002-12-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dihydroneopterin aldolase
ID:FOLB_MYCTU
AC:P9WNC5
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
B59 %
C41 %


Ligand binding site composition:

B-Factor:37.083
Number of residues:23
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.732340.875

% Hydrophobic% Polar
59.4140.59
According to VolSite

Ligand :
1nbu_2 Structure
HET Code: PH2
Formula: C7H9N5O2
Molecular weight: 195.179 g/mol
DrugBank ID: DB02119
Buried Surface Area:78.1 %
Polar Surface area: 112.1 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 4
Rings: 2
Aromatic rings: 0
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 1

Mass center Coordinates

XYZ
3.8101423.196729.1773


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
C11CG1VAL- 183.30Hydrophobic
O4NVAL- 182.89165.18H-Bond
(Protein Donor)
O4OE1GLU- 223.35140.83H-Bond
(Ligand Donor)
O4OE2GLU- 223.22163.6H-Bond
(Ligand Donor)
N6OTYR- 522.85162.68H-Bond
(Ligand Donor)
N5NTYR- 543.17169.11H-Bond
(Protein Donor)
C11CZTYR- 544.460Hydrophobic
DuArDuArTYR- 543.850Aromatic Face/Face
O8NILE- 732.98165.54H-Bond
(Protein Donor)
N6OE2GLU- 742.82147.68H-Bond
(Ligand Donor)
N7OE2GLU- 743.44129.53H-Bond
(Ligand Donor)
N7OE1GLU- 742.92162.13H-Bond
(Ligand Donor)
O8OHOH- 90232.58166.1H-Bond
(Protein Donor)