scPDB - 2ykj entry

Protein Data Bank Entry:

PDB ID : 2ykj

Resolution :1.460 Å

Experimental Method : X-ray

Deposition Date : 2011-05-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Heat shock protein HSP 90-alpha
ID:	HS90A_HUMAN
AC:	P07900
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:	12.373
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.334	803.250

% Hydrophobic	% Polar
53.36	46.64
According to VolSite

Ligand :

HET Code:	YKJ
Formula:	C25H18N6O
Molecular weight:	418.450 g/mol
DrugBank ID:	-
Buried Surface Area:	69.73 %
Polar Surface area:	109.58 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	6
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
5.79022	12.7461	25.3633

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
C3	CG1	ILE- 26	4.49	0	Hydrophobic	false
C14	CB	ASN- 51	4.12	0	Hydrophobic	false
C25	SD	MET- 98	3.55	0	Hydrophobic	false
C12	CE	MET- 98	3.83	0	Hydrophobic	false
C8	SD	MET- 98	3.7	0	Hydrophobic	false
N2	O	LEU- 103	2.7	136.9	H-Bond (Ligand Donor)	false
C9	CD2	LEU- 103	3.63	0	Hydrophobic	false
C6	CB	LEU- 107	4.39	0	Hydrophobic	false
C7	CB	LEU- 107	4.07	0	Hydrophobic	false
C18	CD1	LEU- 107	3.74	0	Hydrophobic	false
C19	CD2	LEU- 107	4.11	0	Hydrophobic	false
C21	CB	LEU- 107	3.66	0	Hydrophobic	false
C22	CD2	LEU- 107	4.1	0	Hydrophobic	false
C22	CG2	ILE- 110	4.34	0	Hydrophobic	false
C3	CB	ALA- 111	3.8	0	Hydrophobic	false
C22	CB	ALA- 111	4.24	0	Hydrophobic	false
C24	CB	PHE- 138	3.63	0	Hydrophobic	false
N3	OH	TYR- 139	2.68	149.29	H-Bond (Protein Donor)	false
C9	CG2	VAL- 150	4.04	0	Hydrophobic	false
C9	CB	TRP- 162	4.29	0	Hydrophobic	false
C10	CE2	TRP- 162	3.33	0	Hydrophobic	false
C14	CG2	THR- 184	4.08	0	Hydrophobic	false
N5	O	HOH- 2185	2.7	165.74	H-Bond (Protein Donor)	false