scPDB - 2ykb entry

Protein Data Bank Entry:

PDB ID : 2ykb

Resolution :1.930 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:	13.450
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.484	772.875

% Hydrophobic	% Polar
56.77	43.23
According to VolSite

Ligand :

HET Code:	YKB
Formula:	C23H19N5O2
Molecular weight:	397.429 g/mol
DrugBank ID:	-
Buried Surface Area:	71.47 %
Polar Surface area:	113.76 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
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
6.1399	32.513	-25.2397

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
C19	CD1	ILE- 26	3.49	0	Hydrophobic	false
C27	CB	ASN- 51	3.78	0	Hydrophobic	false
N30	OD2	ASP- 93	2.8	143.44	H-Bond (Ligand Donor)	false
C25	SD	MET- 98	3.72	0	Hydrophobic	false
C10	SD	MET- 98	3.7	0	Hydrophobic	false
N16	O	LEU- 103	2.55	138.23	H-Bond (Ligand Donor)	false
C11	CD2	LEU- 103	3.42	0	Hydrophobic	false
C13	CB	LEU- 107	4.07	0	Hydrophobic	false
C17	CB	LEU- 107	4.42	0	Hydrophobic	false
C4	CB	LEU- 107	3.68	0	Hydrophobic	false
C8	CD1	LEU- 107	3.82	0	Hydrophobic	false
C3	CD2	LEU- 107	4.1	0	Hydrophobic	false
C1	CG2	ILE- 110	4.19	0	Hydrophobic	false
C19	CB	ALA- 111	3.98	0	Hydrophobic	false
C4	CB	ALA- 111	3.98	0	Hydrophobic	false
C1	CG1	VAL- 136	4.25	0	Hydrophobic	false
C3	CB	PHE- 138	3.83	0	Hydrophobic	false
N15	OH	TYR- 139	2.73	152.37	H-Bond (Protein Donor)	false
C11	CG2	VAL- 150	4.08	0	Hydrophobic	false
C11	CB	TRP- 162	4.23	0	Hydrophobic	false
C12	CE2	TRP- 162	3.37	0	Hydrophobic	false
O29	O	HOH- 2138	2.64	171.21	H-Bond (Protein Donor)	false