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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:

3dop

2.000 Å

X-ray

2008-07-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:3-oxo-5-beta-steroid 4-dehydrogenase
ID:AK1D1_HUMAN
AC:P51857
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:19.559
Number of residues:45
Including
Standard Amino Acids: 44
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.3121113.750

% Hydrophobic% Polar
51.5248.48
According to VolSite

Created with Highcharts 4.0.1Chart context menuDistribution of cavity propertiesscPDB Median3dopHydrophobicAromaticHBond AcceptorHBond DonorHBondAcceptor/DonorPositive IonizableNegativeIonizableDummy802040Highcharts.com
Ligand :
3dop_2 Structure
HET Code: NAP
Formula: C21H25N7O17P3
Molecular weight: 740.381 g/mol
DrugBank ID: DB03461
Buried Surface Area:67.11 %
Polar Surface area: 405.54 Å2
Number of
H-Bond Acceptors: 21
H-Bond Donors: 5
Rings: 5
Aromatic rings: 3
Anionic atoms: 4
Cationic atoms: 1
Rule of Five Violation: 2
Rotatable Bonds: 13

Mass center Coordinates

XYZ
5.42431-16.32832.09556
Created with Highcharts 4.0.1Chart context menuDistribution of ligand propertiesscPDB Median3dopRingsAromatic 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
O2DNTHR- 253.23144.43H-Bond
(Protein Donor)
O3DNTYR- 262.96150.13H-Bond
(Protein Donor)
C3DCBTYR- 263.870Hydrophobic
O2DOD2ASP- 532.59179.01H-Bond
(Ligand Donor)
C2DCE2TYR- 583.790Hydrophobic
N7NOGSER- 1692.97126.36H-Bond
(Ligand Donor)
O7NND2ASN- 1702.76154.71H-Bond
(Protein Donor)
N7NOE1GLN- 1933.24145.62H-Bond
(Ligand Donor)
DuArDuArTYR- 2193.780Aromatic Face/Face
C3NCBTYR- 2194.130Hydrophobic
O1NOGSER- 2202.92155.38H-Bond
(Protein Donor)
O5DNSER- 2203.1128.12H-Bond
(Protein Donor)
O1ANLEU- 2222.93141.34H-Bond
(Protein Donor)
O1ANTHR- 2243.06154.53H-Bond
(Protein Donor)
C3BCBSER- 2253.840Hydrophobic
C4DCG1ILE- 2714.180Hydrophobic
O2ANLYS- 2732.93172.88H-Bond
(Protein Donor)
O1XNZLYS- 2732.75175.68H-Bond
(Protein Donor)
C3DCBLYS- 2734.250Hydrophobic
C3BCDLYS- 2734.370Hydrophobic
C5DCBLYS- 2734.010Hydrophobic
O1XNZLYS- 2732.750Ionic
(Protein Cationic)
O3XOGSER- 2742.7170.57H-Bond
(Protein Donor)
O1XNPHE- 2752.92156.8H-Bond
(Protein Donor)
O2XNH2ARG- 2793.03165.77H-Bond
(Protein Donor)
O3XNEARG- 2792.79172.71H-Bond
(Protein Donor)
O2XCZARG- 2793.90Ionic
(Protein Cationic)
O3XCZARG- 2793.650Ionic
(Protein Cationic)
N6AOE1GLU- 2822.97157.12H-Bond
(Ligand Donor)
N7AND2ASN- 2833.01173.08H-Bond
(Protein Donor)
N6AOD1ASN- 2832.83147.75H-Bond
(Ligand Donor)