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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:

3ntd

1.990 Å

X-ray

2010-07-03

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:FAD-dependent pyridine nucleotide-disulphide oxidoreductase
ID:A3QAV3_SHELP
AC:A3QAV3
Organism:Shewanella loihica
Reign:Bacteria
TaxID:323850
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A9 %
B91 %


Ligand binding site composition:

B-Factor:29.966
Number of residues:62
Including
Standard Amino Acids: 57
Non Standard Amino Acids: 1
Water Molecules: 4
Cofactors: COA
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.3651265.625

% Hydrophobic% Polar
47.7352.27
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3ntdHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy80204060Highcharts.com
Ligand :
3ntd_2 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:75.69 %
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
9.29494-46.42426.2643
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3ntdRingsAromatic 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
C4BCG2VAL- 103.980Hydrophobic
C4'CBALA- 113.850Hydrophobic
O1PNGLY- 122.95149.09H-Bond
(Protein Donor)
O3BOE2GLU- 333130.44H-Bond
(Ligand Donor)
O3BOE1GLU- 332.77161.67H-Bond
(Ligand Donor)
O2BOE2GLU- 332.71172.11H-Bond
(Ligand Donor)
N3ANARG- 343.11140.89H-Bond
(Protein Donor)
C2BCDARG- 343.620Hydrophobic
O2AND2ASN- 423.18160.49H-Bond
(Protein Donor)
C8CBASN- 424.10Hydrophobic
C6CBCYS- 434.430Hydrophobic
C9ASGCYS- 433.960Hydrophobic
C7MCGPRO- 464.280Hydrophobic
N6AOVAL- 812.93158.86H-Bond
(Ligand Donor)
N1ANVAL- 813.04160.3H-Bond
(Protein Donor)
O1POGSER- 1122.89137.44H-Bond
(Protein Donor)
C7MCD2LEU- 1333.710Hydrophobic
O1ANH2ARG- 1342.97172.86H-Bond
(Protein Donor)
O1ACZARG- 1343.820Ionic
(Protein Cationic)
C1'CZPHE- 1614.480Hydrophobic
C7CG1ILE- 1623.660Hydrophobic
C8CD1ILE- 1623.650Hydrophobic
O3'OD1ASP- 3032.94162.99H-Bond
(Ligand Donor)
O3'OD2ASP- 3033.47135.19H-Bond
(Ligand Donor)
C5'CBASP- 3034.260Hydrophobic
O2PNASP- 3032.73165.73H-Bond
(Protein Donor)
N1NALA- 3213.46127.85H-Bond
(Protein Donor)
O2NALA- 3212.89176.09H-Bond
(Protein Donor)
C2'CBALA- 3213.930Hydrophobic
C5'CBALA- 3244.180Hydrophobic
N3OTYR- 4462.82164.82H-Bond
(Ligand Donor)
O1POHOH- 5752.64179.94H-Bond
(Protein Donor)
O2POHOH- 5852.92179.96H-Bond
(Protein Donor)
C2'C2PCOA- 9014.190Hydrophobic