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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:

3i6q

1.870 Å

X-ray

2009-07-07

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Putative leucoanthocyanidin reductase 1
ID:Q4W2K4_VITVI
AC:Q4W2K4
Organism:Vitis vinifera
Reign:Eukaryota
TaxID:29760
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:18.187
Number of residues:41
Including
Standard Amino Acids: 39
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.061722.250

% Hydrophobic% Polar
43.4656.54
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3i6qHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3i6q_1 Structure
HET Code: NDP
Formula: C21H26N7O17P3
Molecular weight: 741.389 g/mol
DrugBank ID: DB02338
Buried Surface Area:51.91 %
Polar Surface area: 404.9 Å2
Number of
H-Bond Acceptors: 22
H-Bond Donors: 5
Rings: 5
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
3.196798.3174619.053
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3i6qRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation80102030Highcharts.com


Binding mode :
What is Poseview ?
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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
O3BOG1THR- 193.08143.05H-Bond
(Protein Donor)
O2ANPHE- 212.95165.38H-Bond
(Protein Donor)
O2NNILE- 222.86171.25H-Bond
(Protein Donor)
C1DCG1ILE- 224.490Hydrophobic
C5DCG1ILE- 224.080Hydrophobic
N1ANILE- 693.01166.47H-Bond
(Protein Donor)
N6AOD1ASN- 702.99148.48H-Bond
(Ligand Donor)
C1BCG1VAL- 914.420Hydrophobic
N6AOD2ASP- 982.98149.09H-Bond
(Ligand Donor)
O3DOGSER- 1182.87163.02H-Bond
(Ligand Donor)
C4DCBPHE- 1204.480Hydrophobic
C1DCBPHE- 1204.230Hydrophobic
N7NOPHE- 1202.84161.8H-Bond
(Ligand Donor)
O2DNZLYS- 1402.86157.58H-Bond
(Protein Donor)
N7NOASN- 1602.63147.9H-Bond
(Ligand Donor)
O7NNILE- 1622.99174.42H-Bond
(Protein Donor)
O1AOHOH- 4592.7179.99H-Bond
(Protein Donor)