scPDB - 3gki entry

Protein Data Bank Entry:

PDB ID : 3gki

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2009-03-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Niemann-Pick C1 protein
ID:	NPC1_HUMAN
AC:	O15118
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:	33.700
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.287	587.250

% Hydrophobic	% Polar
54.02	45.98
According to VolSite

Ligand :

HET Code:	CLR
Formula:	C27H46O
Molecular weight:	386.654 g/mol
DrugBank ID:	DB04540
Buried Surface Area:	79.05 %
Polar Surface area:	20.23 Å2

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

Mass center Coordinates

X	Y	Z
-35.7964	-27.6769	2.90821

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
O1	O	HOH- 5	3.09	146.01	H-Bond (Ligand Donor)	false
C4	CH2	TRP- 27	4.33	0	Hydrophobic	false
O1	ND2	ASN- 41	2.87	136.04	H-Bond (Protein Donor)	false
O1	NE2	GLN- 79	3	159.59	H-Bond (Protein Donor)	false
C19	CG2	THR- 82	3.94	0	Hydrophobic	false
C2	CG2	THR- 82	4	0	Hydrophobic	false
C1	CB	LEU- 83	3.79	0	Hydrophobic	false
C11	CD1	LEU- 83	3.8	0	Hydrophobic	false
C19	CB	ASN- 86	4.4	0	Hydrophobic	false
C21	CB	ASN- 86	4.47	0	Hydrophobic	false
C18	CB	ASN- 86	3.56	0	Hydrophobic	false
C12	CD1	LEU- 87	3.97	0	Hydrophobic	false
C21	CD1	LEU- 87	4.5	0	Hydrophobic	false
C21	CG	PRO- 90	3.54	0	Hydrophobic	false
C9	CD1	PHE- 108	4.05	0	Hydrophobic	false
C13	CE1	PHE- 108	3.64	0	Hydrophobic	false
C14	CE1	PHE- 108	3.55	0	Hydrophobic	false
C15	CE1	PHE- 108	3.41	0	Hydrophobic	false
C17	CZ	PHE- 108	3.33	0	Hydrophobic	false
C7	CD2	LEU- 111	3.69	0	Hydrophobic	false
C3	CG2	THR- 112	3.61	0	Hydrophobic	false
C23	CD2	LEU- 176	4.32	0	Hydrophobic	false
C27	CD2	LEU- 176	3.6	0	Hydrophobic	false
C27	CE2	TYR- 192	3.6	0	Hydrophobic	false
C16	CB	MET- 193	4.28	0	Hydrophobic	false
C22	SD	MET- 193	3.83	0	Hydrophobic	false
C27	CG	MET- 193	3.76	0	Hydrophobic	false
C23	CG	MET- 193	3.94	0	Hydrophobic	false
C15	CD1	PHE- 194	4.26	0	Hydrophobic	false
C26	CB	ASN- 198	3.93	0	Hydrophobic	false
C18	CG	GLN- 200	4.11	0	Hydrophobic	false
C24	CG	GLN- 200	3.98	0	Hydrophobic	false
C20	CG	GLN- 200	4.1	0	Hydrophobic	false
C26	CB	GLN- 200	3.97	0	Hydrophobic	false
C15	CB	ALA- 201	3.65	0	Hydrophobic	false
C19	CG	PRO- 202	3.54	0	Hydrophobic	false
C4	CZ	PHE- 203	3.55	0	Hydrophobic	false
C7	CD1	ILE- 205	3.75	0	Hydrophobic	false
C15	CD1	ILE- 205	4.46	0	Hydrophobic	false