scPDB - 1afs entry

Protein Data Bank Entry:

PDB ID : 1afs

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1997-03-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-alpha-hydroxysteroid dehydrogenase
ID:	DIDH_RAT
AC:	P23457
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	1.1.1.50

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	26.691
Number of residues:	21
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.854	664.875

% Hydrophobic	% Polar
45.18	54.82
According to VolSite

Ligand :

HET Code:	TES
Formula:	C19H28O2
Molecular weight:	288.424 g/mol
DrugBank ID:	DB00624
Buried Surface Area:	56.05 %
Polar Surface area:	37.29 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	4
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	0

Mass center Coordinates

X	Y	Z
-24.1596	9.10657	-1.87424

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C9	CD2	LEU- 54	3.76	0	Hydrophobic	false
O3	OH	TYR- 55	2.55	155.87	H-Bond (Protein Donor)	false
O3	NE2	HIS- 117	2.77	134.72	H-Bond (Protein Donor)	false
C2	CE2	PHE- 118	3.96	0	Hydrophobic	false
C12	CE1	PHE- 129	3.8	0	Hydrophobic	false
C15	CB	THR- 226	4.47	0	Hydrophobic	false
C6	CE2	TRP- 227	3.93	0	Hydrophobic	false
C18	CB	TRP- 227	3.7	0	Hydrophobic	false
C19	CD2	TRP- 227	3.93	0	Hydrophobic	false
C11	CZ	TYR- 310	3.57	0	Hydrophobic	false
C12	CG	TYR- 310	4.3	0	Hydrophobic	false
C18	CD2	TYR- 310	4.17	0	Hydrophobic	false
C19	CZ	TYR- 310	3.66	0	Hydrophobic	false
C2	C4N	NAP- 324	3.64	0	Hydrophobic	false