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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:

3o9l

2.400 Å

X-ray

2010-08-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Renin
ID:RENI_HUMAN
AC:P00797
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:3.4.23.15


Chains:

Chain Name:Percentage of Residues
within binding site
C83 %
D17 %


Ligand binding site composition:

B-Factor:38.250
Number of residues:42
Including
Standard Amino Acids: 41
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.263833.625

% Hydrophobic% Polar
56.2843.72
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3o9lHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3o9l_2 Structure
HET Code: LPN
Formula: C35H42Cl3N2O4
Molecular weight: 661.078 g/mol
DrugBank ID: -
Buried Surface Area:67.19 %
Polar Surface area: 64.61 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 1
Rings: 5
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 14

Mass center Coordinates

XYZ
-7.57302-15.4731-9.94641
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3o9lRingsAromatic RingsHBond AcceptorHBond DonorRotatable BondsPositive IonizableNegativeIonizableRO5 Violation8051015Highcharts.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
C39CGGLN- 194.420Hydrophobic
C42CBGLN- 194.210Hydrophobic
C44CBTYR- 203.810Hydrophobic
C42CG2VAL- 364.270Hydrophobic
C44CG2VAL- 363.910Hydrophobic
C32CG1VAL- 363.860Hydrophobic
N28OD1ASP- 383.4147.18H-Bond
(Ligand Donor)
N28OD2ASP- 383.41159.15H-Bond
(Ligand Donor)
N28OD1ASP- 383.40Ionic
(Ligand Cationic)
N28OD2ASP- 383.410Ionic
(Ligand Cationic)
C31CBASP- 384.280Hydrophobic
C18CBSER- 414.20Hydrophobic
C22CBSER- 414.320Hydrophobic
CL1CBTRP- 454.470Hydrophobic
C8CBTRP- 454.060Hydrophobic
C4CGPRO- 473.780Hydrophobic
CL1CGPRO- 473.80Hydrophobic
C14CD1LEU- 813.870Hydrophobic
C8CG1VAL- 884.380Hydrophobic
CL1CG2VAL- 1113.480Hydrophobic
C4CEMET- 1143.870Hydrophobic
C8CEMET- 1143.730Hydrophobic
C2CEMET- 1143.40Hydrophobic
CL36CGPRO- 1183.980Hydrophobic
CL9CE1PHE- 1193.920Hydrophobic
CL36CD1PHE- 1193.660Hydrophobic
C12CE1PHE- 1193.890Hydrophobic
C37CBALA- 1223.830Hydrophobic
CL9CE2PHE- 1243.740Hydrophobic
C32CZPHE- 1243.890Hydrophobic
C34CZPHE- 1243.390Hydrophobic
CL9CG1VAL- 1274.420Hydrophobic
C12CG1VAL- 1274.140Hydrophobic
C16CG1VAL- 1274.190Hydrophobic
C31CG2VAL- 1273.910Hydrophobic
N28OD1ASP- 2263.940Ionic
(Ligand Cationic)
N28OD2ASP- 2263.390Ionic
(Ligand Cationic)
N28OD2ASP- 2263.39160.81H-Bond
(Ligand Donor)
C40CBSER- 2304.210Hydrophobic