scPDB - 1olm entry

Protein Data Bank Entry:

PDB ID : 1olm

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2003-08-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	SEC14-like protein 2
ID:	S14L2_HUMAN
AC:	O76054
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	15.978
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.952	789.750

% Hydrophobic	% Polar
77.78	22.22
According to VolSite

Ligand :

HET Code:	VTQ
Formula:	C29H50O3
Molecular weight:	446.705 g/mol
DrugBank ID:	-
Buried Surface Area:	65.08 %
Polar Surface area:	54.37 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	1
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
-21.6968	24.0692	91.5462

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
C13	CD1	LEU- 84	4.13	0	Hydrophobic	false
C10	CD1	ILE- 103	4.46	0	Hydrophobic	false
C10	CD2	LEU- 106	3.98	0	Hydrophobic	false
C8	CD2	LEU- 106	3.68	0	Hydrophobic	false
C12	CB	ALA- 108	4.15	0	Hydrophobic	false
C12	CD2	LEU- 120	3.81	0	Hydrophobic	false
C13	CD2	LEU- 120	3.86	0	Hydrophobic	false
C13	CD	LYS- 124	4.07	0	Hydrophobic	false
O2	NZ	LYS- 124	3.41	135.12	H-Bond (Protein Donor)	false
C1	CD1	TYR- 153	4.13	0	Hydrophobic	false
C25	CE2	TYR- 153	4	0	Hydrophobic	false
C29	CE2	TYR- 153	4.31	0	Hydrophobic	false
C21	CE1	TYR- 153	3.71	0	Hydrophobic	false
C22	CZ	TYR- 153	3.43	0	Hydrophobic	false
C19	SG	CYS- 155	4.27	0	Hydrophobic	false
C15	CD1	LEU- 158	4.5	0	Hydrophobic	false
C17	CD1	LEU- 158	3.99	0	Hydrophobic	false
C19	CD2	LEU- 158	4.23	0	Hydrophobic	false
O3	O	HIS- 162	2.85	159.65	H-Bond (Ligand Donor)	false
C15	CB	HIS- 162	4.13	0	Hydrophobic	false
C14	CG2	VAL- 168	3.78	0	Hydrophobic	false
C8	CE1	TYR- 171	3.5	0	Hydrophobic	false
C16	CD2	TYR- 171	4.39	0	Hydrophobic	false
C20	CE2	TYR- 171	4.18	0	Hydrophobic	false
C22	CE2	TYR- 171	4.34	0	Hydrophobic	false
C14	CD2	TYR- 171	4.29	0	Hydrophobic	false
C11	CG	TYR- 171	3.56	0	Hydrophobic	false
C29	CE2	PHE- 174	4	0	Hydrophobic	false
C26	CD2	LEU- 175	3.94	0	Hydrophobic	false
C28	CE2	PHE- 178	3.51	0	Hydrophobic	false
C1	CD2	LEU- 189	3.72	0	Hydrophobic	false
C27	CD1	LEU- 189	3.77	0	Hydrophobic	false
C1	CG2	VAL- 191	3.98	0	Hydrophobic	false
C19	CE1	PHE- 198	3.62	0	Hydrophobic	false
C21	CE1	PHE- 198	4.49	0	Hydrophobic	false
C19	CB	ALA- 201	3.96	0	Hydrophobic	false
C21	CD1	TYR- 202	4.45	0	Hydrophobic	false
C23	CD1	TYR- 202	4.48	0	Hydrophobic	false
C14	CG2	ILE- 205	4.38	0	Hydrophobic	false
C20	CG1	ILE- 205	4.03	0	Hydrophobic	false
C23	CD1	ILE- 205	3.79	0	Hydrophobic	false
C24	CD1	LEU- 209	3.93	0	Hydrophobic	false
C26	CD2	LEU- 209	4.16	0	Hydrophobic	false
C26	CG2	THR- 213	4.46	0	Hydrophobic	false
C24	CD1	ILE- 217	3.95	0	Hydrophobic	false