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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:

4h2p

1.980 Å

X-ray

2012-09-13

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase
ID:Q988D3_RHILO
AC:Q988D3
Organism:Rhizobium loti
Reign:Bacteria
TaxID:266835
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:21.605
Number of residues:68
Including
Standard Amino Acids: 61
Non Standard Amino Acids: 0
Water Molecules: 7
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.7411674.000

% Hydrophobic% Polar
42.5457.46
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median4h2pHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
4h2p_3 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:63.12 %
Polar Surface area: 381.7 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 7
Rings: 6
Aromatic rings: 3
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 3
Rotatable Bonds: 13

Mass center Coordinates

XYZ
-57.3282-13.4895-19.8279
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median4h2pRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80102030Highcharts.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
C4'CD2PHE- 214.30Hydrophobic
O1PNALA- 222.83159.32H-Bond
(Protein Donor)
O2BOE1GLU- 412.94166.12H-Bond
(Ligand Donor)
N3ANLYS- 423.19142.25H-Bond
(Protein Donor)
N3OTYR- 542.78158.81H-Bond
(Ligand Donor)
O4NTYR- 542.91168.35H-Bond
(Protein Donor)
O2'NH1ARG- 1062.97143.98H-Bond
(Protein Donor)
O2'NH2ARG- 1062.96145.24H-Bond
(Protein Donor)
N6AOALA- 1303.08168.8H-Bond
(Ligand Donor)
N1ANALA- 1303.05148.27H-Bond
(Protein Donor)
C7MCD2LEU- 1793.640Hydrophobic
C7MCDARG- 1813.720Hydrophobic
C7MCE2TYR- 2704.160Hydrophobic
O3'OD1ASP- 2882.76173.32H-Bond
(Ligand Donor)
C5'CBASP- 2884.130Hydrophobic
O2PNASP- 2882.89162.43H-Bond
(Protein Donor)
C7MCGPRO- 2954.170Hydrophobic
C6CBPRO- 2953.660Hydrophobic
N1NALA- 3013.01169.4H-Bond
(Protein Donor)
O2NALA- 3012.92124.36H-Bond
(Protein Donor)
C4'CBALA- 3014.040Hydrophobic
C2'CBALA- 3014.140Hydrophobic
O2NGLY- 3023.05144.48H-Bond
(Protein Donor)
O1POHOH- 5022.61170.54H-Bond
(Protein Donor)
O2POHOH- 5032.7179.99H-Bond
(Protein Donor)
O2AOHOH- 5062.65179.98H-Bond
(Protein Donor)