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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:

1lbm

2.800 Å

X-ray

2002-04-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:N-(5'-phosphoribosyl)anthranilate isomerase
ID:TRPF_THEMA
AC:Q56320
Organism:Thermotoga maritima
Reign:Bacteria
TaxID:243274
EC Number:5.3.1.24


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:24.009
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.107293.625

% Hydrophobic% Polar
34.4865.52
According to VolSite

Ligand :
1lbm_1 Structure
HET Code: 137
Formula: C12H15NO9P
Molecular weight: 348.223 g/mol
DrugBank ID: DB03543
Buried Surface Area:62.16 %
Polar Surface area: 195.08 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 4
Rings: 1
Aromatic rings: 1
Anionic atoms: 3
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 9

Mass center Coordinates

XYZ
11.464630.892863.0752


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
C1'SGCYS- 73.780Hydrophobic
C1'CG2VAL- 294.290Hydrophobic
C2CG2VAL- 293.970Hydrophobic
C6CG1VAL- 294.170Hydrophobic
C6CBSER- 343.870Hydrophobic
O71OGSER- 342.88155.47H-Bond
(Protein Donor)
O71NEARG- 363.06170.08H-Bond
(Protein Donor)
O72NEARG- 362.85121H-Bond
(Protein Donor)
O71CZARG- 363.940Ionic
(Protein Cationic)
O72CZARG- 363.890Ionic
(Protein Cationic)
C1'CG2VAL- 594.290Hydrophobic
C3CG1VAL- 593.790Hydrophobic
C4CG2VAL- 614.150Hydrophobic
O2'OE1GLN- 812.97157.73H-Bond
(Ligand Donor)
O4'OD1ASP- 1263.22138.28H-Bond
(Ligand Donor)
O1PNGLY- 1592.58150.1H-Bond
(Protein Donor)
O3'OD2ASP- 1783.13170.15H-Bond
(Ligand Donor)
O3PNSER- 1802.87155.1H-Bond
(Protein Donor)
O3'OGSER- 1802.98147.16H-Bond
(Protein Donor)
C3'CBSER- 1804.40Hydrophobic
O2POGSER- 1813.14168.68H-Bond
(Protein Donor)
O3PNSER- 1812.79148.92H-Bond
(Protein Donor)
O3POGSER- 1813.34122.06H-Bond
(Protein Donor)
O3POHOH- 4033.43145.99H-Bond
(Protein Donor)