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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:

2c94

1.900 Å

X-ray

2005-12-09

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:6,7-dimethyl-8-ribityllumazine synthase
ID:RISB_MYCTU
AC:P9WHE9
Organism:Mycobacterium tuberculosis
Reign:Bacteria
TaxID:83332
EC Number:2.5.1.78


Chains:

Chain Name:Percentage of Residues
within binding site
A36 %
E64 %


Ligand binding site composition:

B-Factor:30.017
Number of residues:41
Including
Standard Amino Acids: 39
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.732637.875

% Hydrophobic% Polar
44.9755.03
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median2c94HydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
2c94_5 Structure
HET Code: TSF
Formula: C15H21F2N4O10P
Molecular weight: 486.319 g/mol
DrugBank ID: -
Buried Surface Area:71.14 %
Polar Surface area: 235.67 Å2
Number of
H-Bond Acceptors: 10
H-Bond Donors: 6
Rings: 2
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 11

Mass center Coordinates

XYZ
52.9215-17.051211.0928
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median2c94RingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.com


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
O1OGSER- 253.09150.83H-Bond
(Protein Donor)
C15CZ3TRP- 273.480Hydrophobic
C10CE2TRP- 274.480Hydrophobic
O1NALA- 592.89137.02H-Bond
(Protein Donor)
O19NILE- 603.13174.27H-Bond
(Protein Donor)
C13CG1ILE- 604.420Hydrophobic
C12CG1ILE- 603.810Hydrophobic
O26OE2GLU- 612.7163.26H-Bond
(Ligand Donor)
N3OVAL- 812.73174.4H-Bond
(Ligand Donor)
C16CG1VAL- 824.360Hydrophobic
O2PNGLN- 863171.67H-Bond
(Protein Donor)
O3POG1THR- 872.61171.53H-Bond
(Protein Donor)
O3PNTHR- 872.78155.93H-Bond
(Protein Donor)
O1POG1THR- 873.5125.79H-Bond
(Protein Donor)
C18CBHIS- 893.850Hydrophobic
C17CBPHE- 904.340Hydrophobic
C10CG2VAL- 934.430Hydrophobic
C14CBALA- 1134.10Hydrophobic
O23OASN- 1142.81161.19H-Bond
(Ligand Donor)
O26NASN- 1142.74157.95H-Bond
(Protein Donor)
O2PNH2ARG- 1283.22153.95H-Bond
(Protein Donor)
O1PNEARG- 1283.1160.5H-Bond
(Protein Donor)
O1PNH2ARG- 1283.46138.82H-Bond
(Protein Donor)
O1PCZARG- 1283.730Ionic
(Protein Cationic)
C14CBALA- 1424.230Hydrophobic
C14CBALA- 1454.070Hydrophobic
O2OHOH- 21152.64174.93H-Bond
(Protein Donor)
O3POHOH- 21172.53179.99H-Bond
(Protein Donor)