scPDB - 4qim entry

Protein Data Bank Entry:

PDB ID : 4qim

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2014-05-31

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:	0.000
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.722	600.750

% Hydrophobic	% Polar
55.06	44.94
According to VolSite

Ligand :

HET Code:	A8T
Formula:	C27H29N5O
Molecular weight:	439.552 g/mol
DrugBank ID:	-
Buried Surface Area:	74.77 %
Polar Surface area:	65.38 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
13.8382	-12.6887	-22.8147

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
C12	CD1	ILE- 215	4.39	0	Hydrophobic	false
C13	CD1	ILE- 215	3.79	0	Hydrophobic	false
N1	ND2	ASN- 219	3.1	144.96	H-Bond (Protein Donor)	false
C12	CG	LEU- 221	4.19	0	Hydrophobic	false
C2	CD1	LEU- 221	3.93	0	Hydrophobic	false
C19	CE	MET- 230	3.73	0	Hydrophobic	false
C12	SD	MET- 301	4.26	0	Hydrophobic	false
C13	SD	MET- 301	4.01	0	Hydrophobic	false
C13	CD2	LEU- 303	4.36	0	Hydrophobic	false
C26	CD2	LEU- 325	4.22	0	Hydrophobic	false
C8	CB	ASP- 384	4.08	0	Hydrophobic	false
C18	CG2	VAL- 386	3.49	0	Hydrophobic	false
C19	CB	SER- 387	3.73	0	Hydrophobic	false
C24	CD1	ILE- 389	3.75	0	Hydrophobic	false
C25	CZ	PHE- 391	3.43	0	Hydrophobic	false
C9	CG	TYR- 394	4.35	0	Hydrophobic	false
C8	CD1	TYR- 394	3.63	0	Hydrophobic	false
C7	CD1	TYR- 394	4.21	0	Hydrophobic	false
C13	CG	LYS- 395	3.8	0	Hydrophobic	false
C1	CG	LYS- 395	3.98	0	Hydrophobic	false
O1	NZ	LYS- 395	2.84	131.26	H-Bond (Protein Donor)	false
N5	NH2	ARG- 400	3.08	172.52	H-Bond (Protein Donor)	false
N4	NH2	ARG- 400	2.72	138.76	H-Bond (Protein Donor)	false
C12	CZ	PHE- 484	3.93	0	Hydrophobic	false
C6	CG	PRO- 513	4.22	0	Hydrophobic	false
C20	CB	GLU- 518	3.56	0	Hydrophobic	false
C14	CG	GLU- 518	3.65	0	Hydrophobic	false
C21	CB	ASN- 521	4.37	0	Hydrophobic	false
C20	CD1	LEU- 522	4.03	0	Hydrophobic	false