scPDB - 4jkv entry

Protein Data Bank Entry:

PDB ID : 4jkv

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2013-03-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Smoothened homolog
ID:	SMO_HUMAN
AC:	Q99835
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:	58.011
Number of residues:	47
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.015	978.750

% Hydrophobic	% Polar
52.07	47.93
According to VolSite

Ligand :

HET Code:	1KS
Formula:	C26H24F4N6O
Molecular weight:	512.502 g/mol
DrugBank ID:	DB12550
Buried Surface Area:	78.79 %
Polar Surface area:	67.15 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	0
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
-25.6377	23.4214	21.4776

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
O1	ND2	ASN- 219	2.76	170.25	H-Bond (Protein Donor)	false
F3	CG	LEU- 221	4.49	0	Hydrophobic	false
C4	CD1	LEU- 221	4.35	0	Hydrophobic	false
C19	SD	MET- 230	4.09	0	Hydrophobic	false
C20	CG	MET- 230	3.76	0	Hydrophobic	false
C19	CD1	ILE- 234	4.12	0	Hydrophobic	false
C26	CH2	TRP- 281	3.93	0	Hydrophobic	false
C7	CE	MET- 301	3.74	0	Hydrophobic	false
C11	CB	ASP- 384	4.21	0	Hydrophobic	false
C12	CG2	VAL- 386	4.26	0	Hydrophobic	false
C21	CG2	VAL- 386	3.61	0	Hydrophobic	false
C19	CB	SER- 387	3.57	0	Hydrophobic	false
C26	CD1	ILE- 389	3.97	0	Hydrophobic	false
C26	CD2	PHE- 391	3.51	0	Hydrophobic	false
C11	CE1	TYR- 394	4.35	0	Hydrophobic	false
C26	CZ	TYR- 394	4.12	0	Hydrophobic	false
F1	CG	LYS- 395	3.68	0	Hydrophobic	false
N3	NH2	ARG- 400	3.23	123.01	H-Bond (Protein Donor)	false
N3	NH1	ARG- 400	3	127.86	H-Bond (Protein Donor)	false
N4	NH1	ARG- 400	3.18	152.71	H-Bond (Protein Donor)	false
F4	CG	GLN- 477	3.33	0	Hydrophobic	false
F2	CB	TRP- 480	3.5	0	Hydrophobic	false
C2	CG	GLU- 481	4.22	0	Hydrophobic	false
F2	CG	GLU- 481	3.43	0	Hydrophobic	false
F1	CE2	PHE- 484	3.79	0	Hydrophobic	false
C2	CB	PHE- 484	4.38	0	Hydrophobic	false
F2	CB	PHE- 484	4.36	0	Hydrophobic	false
F3	CD1	PHE- 484	4.37	0	Hydrophobic	false
C13	CB	PRO- 513	3.56	0	Hydrophobic	false
C14	CG	PRO- 513	3.7	0	Hydrophobic	false
F3	CG	PRO- 513	3.64	0	Hydrophobic	false
C21	CD2	LEU- 515	4.37	0	Hydrophobic	false
C13	CG	GLU- 518	4.03	0	Hydrophobic	false
C20	CB	GLU- 518	4.08	0	Hydrophobic	false
C16	CG	GLU- 518	3.42	0	Hydrophobic	false
C19	CD1	LEU- 522	3.54	0	Hydrophobic	false