scPDB - 3d0b entry

Protein Data Bank Entry:

PDB ID : 3d0b

Resolution :1.740 Å

Experimental Method : X-ray

Deposition Date : 2008-05-01

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:	18.101
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.035	624.375

% Hydrophobic	% Polar
52.43	47.57
According to VolSite

Ligand :

HET Code:	SNX
Formula:	C22H23N3O3
Molecular weight:	377.436 g/mol
DrugBank ID:	DB08557
Buried Surface Area:	62.13 %
Polar Surface area:	86.35 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
3.089	-11.4741	-24.7623

Binding mode :

What is Poseview ?

2D View
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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
C18	CB	ASN- 51	3.96	0	Hydrophobic	false
C28	CB	ALA- 55	4.38	0	Hydrophobic	false
C28	CD	LYS- 58	3.81	0	Hydrophobic	false
N22	OD2	ASP- 93	2.84	160.83	H-Bond (Ligand Donor)	false
C26	CG2	ILE- 96	4.19	0	Hydrophobic	false
C28	CG2	ILE- 96	4.2	0	Hydrophobic	false
C18	CE	MET- 98	3.75	0	Hydrophobic	false
C25	CG	MET- 98	4.02	0	Hydrophobic	false
C20	SD	MET- 98	3.45	0	Hydrophobic	false
C13	SD	MET- 98	3.7	0	Hydrophobic	false
C12	CD2	LEU- 103	3.66	0	Hydrophobic	false
C25	CD2	LEU- 107	4.26	0	Hydrophobic	false
C20	CD1	LEU- 107	4.32	0	Hydrophobic	false
C1	CD2	LEU- 107	4.14	0	Hydrophobic	false
C3	CB	LEU- 107	4.02	0	Hydrophobic	false
C13	CD1	LEU- 107	4.29	0	Hydrophobic	false
C4	CB	ALA- 111	4.16	0	Hydrophobic	false
C11	CE2	PHE- 138	3.66	0	Hydrophobic	false
C15	CB	PHE- 138	4.48	0	Hydrophobic	false
C13	CZ	PHE- 138	4.14	0	Hydrophobic	false
C1	CB	PHE- 138	3.64	0	Hydrophobic	false
C13	CG1	VAL- 150	4.09	0	Hydrophobic	false
C12	CG2	VAL- 150	4.29	0	Hydrophobic	false
C12	CD2	TRP- 162	3.92	0	Hydrophobic	false
C11	CE2	TRP- 162	3.24	0	Hydrophobic	false
C17	CG2	THR- 184	4.32	0	Hydrophobic	false
C17	CG2	VAL- 186	4.15	0	Hydrophobic	false
O23	O	HOH- 236	2.73	173.65	H-Bond (Protein Donor)	false
O14	O	HOH- 396	3.09	179.95	H-Bond (Protein Donor)	false