scPDB - 2yke entry

Protein Data Bank Entry:

PDB ID : 2yke

Resolution :1.430 Å

Experimental Method : X-ray

Deposition Date : 2011-05-26

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:	8.137
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.194	762.750

% Hydrophobic	% Polar
52.65	47.35
According to VolSite

Ligand :

HET Code:	YKE
Formula:	C29H19N5O
Molecular weight:	453.494 g/mol
DrugBank ID:	-
Buried Surface Area:	70.9 %
Polar Surface area:	83.56 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	7
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
5.41014	12.3739	25.3421

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
C35	CB	ASN- 51	3.67	0	Hydrophobic	false
C28	CB	ALA- 55	3.83	0	Hydrophobic	false
C28	CG2	ILE- 96	4.36	0	Hydrophobic	false
C10	SD	MET- 98	3.78	0	Hydrophobic	false
C27	SD	MET- 98	3.52	0	Hydrophobic	false
C29	CG	MET- 98	3.44	0	Hydrophobic	false
C30	CE	MET- 98	3.85	0	Hydrophobic	false
N15	O	LEU- 103	2.72	141.82	H-Bond (Ligand Donor)	false
C11	CD2	LEU- 103	3.64	0	Hydrophobic	false
C12	CD1	LEU- 107	4.47	0	Hydrophobic	false
C13	CB	LEU- 107	4.04	0	Hydrophobic	false
C18	CB	LEU- 107	4.43	0	Hydrophobic	false
C27	CD1	LEU- 107	4.4	0	Hydrophobic	false
C4	CB	LEU- 107	3.63	0	Hydrophobic	false
C8	CD1	LEU- 107	3.78	0	Hydrophobic	false
C3	CD2	LEU- 107	4.03	0	Hydrophobic	false
C2	CG2	ILE- 110	4.02	0	Hydrophobic	false
C1	CB	ALA- 111	4.06	0	Hydrophobic	false
C1	CG1	VAL- 136	4.31	0	Hydrophobic	false
C6	CB	PHE- 138	3.81	0	Hydrophobic	false
N16	OH	TYR- 139	2.7	155.42	H-Bond (Protein Donor)	false
C11	CG2	VAL- 150	4.08	0	Hydrophobic	false
C11	CB	TRP- 162	4.4	0	Hydrophobic	false
C12	CE2	TRP- 162	3.4	0	Hydrophobic	false
C19	CZ	PHE- 170	3.48	0	Hydrophobic	false
C34	CG2	THR- 184	4.05	0	Hydrophobic	false
N32	O	HOH- 2232	2.82	179.95	H-Bond (Protein Donor)	false