scPDB - 3mnr entry

Protein Data Bank Entry:

PDB ID : 3mnr

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2010-04-22

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
P	100 %

Ligand binding site composition:

B-Factor:	13.451
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.317	742.500

% Hydrophobic	% Polar
57.27	42.73
According to VolSite

Ligand :

HET Code:	SD1
Formula:	C27H31N3O5
Molecular weight:	477.552 g/mol
DrugBank ID:	-
Buried Surface Area:	61.63 %
Polar Surface area:	104.81 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
2.69369	-10.0139	-25.6801

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
C16	CB	ASN- 51	3.66	0	Hydrophobic	false
C35	CB	ASP- 54	3.81	0	Hydrophobic	false
C24	CB	ALA- 55	4.29	0	Hydrophobic	false
O30	NZ	LYS- 58	2.9	147.19	H-Bond (Protein Donor)	false
O32	NZ	LYS- 58	2.97	131.1	H-Bond (Protein Donor)	false
C27	CD	LYS- 58	3.99	0	Hydrophobic	false
N22	OD2	ASP- 93	2.81	161.97	H-Bond (Ligand Donor)	false
C31	CG2	ILE- 96	4.04	0	Hydrophobic	false
C29	CG2	ILE- 96	3.77	0	Hydrophobic	false
C1	SD	MET- 98	4.21	0	Hydrophobic	false
C8	SD	MET- 98	4.01	0	Hydrophobic	false
C17	CE	MET- 98	3.82	0	Hydrophobic	false
C19	SD	MET- 98	3.66	0	Hydrophobic	false
C29	CG	MET- 98	3.96	0	Hydrophobic	false
C7	CD2	LEU- 103	4.08	0	Hydrophobic	false
C8	CD2	LEU- 103	4.05	0	Hydrophobic	false
C8	CD1	LEU- 107	3.83	0	Hydrophobic	false
C13	CD2	LEU- 107	4.07	0	Hydrophobic	false
C33	CD2	LEU- 107	4.22	0	Hydrophobic	false
C19	CD1	LEU- 107	3.72	0	Hydrophobic	false
C29	CD1	LEU- 107	4.46	0	Hydrophobic	false
C26	CD2	LEU- 107	4.3	0	Hydrophobic	false
C1	CG	PHE- 138	3.97	0	Hydrophobic	false
C5	CD2	PHE- 138	3.81	0	Hydrophobic	false
C6	CE2	PHE- 138	4.31	0	Hydrophobic	false
C7	CZ	PHE- 138	4.11	0	Hydrophobic	false
C15	CB	PHE- 138	4.38	0	Hydrophobic	false
C5	CZ	TYR- 139	3.97	0	Hydrophobic	false
O9	OH	TYR- 139	2.68	128.21	H-Bond (Protein Donor)	false
C7	CG2	VAL- 150	4.33	0	Hydrophobic	false
C5	CZ2	TRP- 162	4.44	0	Hydrophobic	false
C7	CE2	TRP- 162	3.5	0	Hydrophobic	false
O21	O	HOH- 458	2.66	167.43	H-Bond (Protein Donor)	false