scPDB - 1kdk entry

Protein Data Bank Entry:

PDB ID : 1kdk

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2001-11-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	9.740	9.740	9.740	0.000	9.740	1

List of CHEMBLId :

CHEMBL27769

Binding Site :

Uniprot Annotation

Name:	Sex hormone-binding globulin
ID:	SHBG_HUMAN
AC:	P04278
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.178
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.132	297.000

% Hydrophobic	% Polar
63.64	36.36
According to VolSite

Ligand :

HET Code:	DHT
Formula:	C19H30O2
Molecular weight:	290.440 g/mol
DrugBank ID:	DB02901
Buried Surface Area:	76.07 %
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
21.8061	10.8124	33.2794

Binding mode :

What is Poseview ?

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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
O3	OG	SER- 42	2.7	170.34	H-Bond (Protein Donor)	false
C4	CE1	PHE- 56	4.04	0	Hydrophobic	false
C6	CE1	PHE- 56	3.9	0	Hydrophobic	false
C16	CB	ASP- 65	4.29	0	Hydrophobic	false
O17	OD1	ASP- 65	2.57	160.21	H-Bond (Ligand Donor)	false
C6	CD2	PHE- 67	3.89	0	Hydrophobic	false
C18	CB	PHE- 67	3.96	0	Hydrophobic	false
C19	CE1	PHE- 67	3.79	0	Hydrophobic	false
C8	CB	PHE- 67	3.73	0	Hydrophobic	false
C18	CG	LEU- 80	4.34	0	Hydrophobic	false
O17	ND2	ASN- 82	2.8	153.55	H-Bond (Protein Donor)	false
C2	CG1	VAL- 105	4.15	0	Hydrophobic	false
C4	CG1	VAL- 105	4.48	0	Hydrophobic	false
C19	CG1	VAL- 105	3.93	0	Hydrophobic	false
C1	CG	MET- 107	3.93	0	Hydrophobic	false
C2	CB	MET- 107	4.36	0	Hydrophobic	false
C11	CG	MET- 107	3.94	0	Hydrophobic	false
C12	SD	MET- 107	4.42	0	Hydrophobic	false
C11	CG2	VAL- 112	4.2	0	Hydrophobic	false
C19	CG1	VAL- 112	4.26	0	Hydrophobic	false
C7	SD	MET- 139	4.06	0	Hydrophobic	false
C14	CE	MET- 139	3.86	0	Hydrophobic	false
C6	CD1	ILE- 141	3.86	0	Hydrophobic	false
C4	CD2	LEU- 171	4.26	0	Hydrophobic	false