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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:

4udq

1.600 Å

X-ray

2014-12-11

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:5-(hydroxymethyl)furfural oxidase
ID:HMFO_METS6
AC:E4QP00
Organism:Methylovorus sp.
Reign:Bacteria
TaxID:887061
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:11.715
Number of residues:65
Including
Standard Amino Acids: 62
Non Standard Amino Acids: 0
Water Molecules: 3
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.978675.000

% Hydrophobic% Polar
44.5055.50
According to VolSite

Ligand :
4udq_1 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:78.7 %
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
35.673313.915139.0676


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
O1ANTHR- 153.12172.78H-Bond
(Protein Donor)
C4'CBTHR- 154.290Hydrophobic
O4'OG1THR- 153.01173.73H-Bond
(Ligand Donor)
O2PNALA- 162.91169.57H-Bond
(Protein Donor)
O3BOE1GLU- 362.7173.77H-Bond
(Ligand Donor)
O2BOE2GLU- 362.68146.73H-Bond
(Ligand Donor)
N3ANALA- 373.14130.96H-Bond
(Protein Donor)
C7MCDARG- 603.760Hydrophobic
O2BNE1TRP- 683.08134.99H-Bond
(Protein Donor)
C2BCZ2TRP- 6840Hydrophobic
C7MCBGLU- 904.150Hydrophobic
C8MCBGLU- 904.310Hydrophobic
O1ANGLY- 982.84162.92H-Bond
(Protein Donor)
C8MCG2VAL- 1014.120Hydrophobic
O2'ND2ASN- 1023.13152.3H-Bond
(Protein Donor)
C9ACBASN- 1023.350Hydrophobic
N5NMET- 1033.18176.41H-Bond
(Protein Donor)
C6CGMET- 1034.370Hydrophobic
N3OVAL- 1052.91145.61H-Bond
(Ligand Donor)
O4NVAL- 1053.2157.37H-Bond
(Protein Donor)
N6AOVAL- 2332.85162.03H-Bond
(Ligand Donor)
N1ANVAL- 2332.99156.07H-Bond
(Protein Donor)
C7MCD2TRP- 4663.610Hydrophobic
C6CE3TRP- 4663.450Hydrophobic
C8CBTRP- 4663.290Hydrophobic
C5'CBALA- 5014.450Hydrophobic
O1PNALA- 5013.08173.2H-Bond
(Protein Donor)
O3'OG1THR- 5122.69169.25H-Bond
(Protein Donor)
N1NASN- 5133.39132.61H-Bond
(Protein Donor)
O2NASN- 5132.75146.62H-Bond
(Protein Donor)
C2'CBASN- 5133.820Hydrophobic
C5'CG2THR- 5164.160Hydrophobic
O2POHOH- 20072.76173.38H-Bond
(Protein Donor)
O2OHOH- 21112.63179.95H-Bond
(Protein Donor)