scPDB - 4dri entry

Protein Data Bank Entry:

PDB ID : 4dri

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2012-02-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine/threonine-protein kinase mTOR	Peptidyl-prolyl cis-trans isomerase FKBP5
ID:	MTOR_HUMAN	FKBP5_HUMAN
AC:	P42345	Q13451
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1	5.2.1.8

Chains:

Chain Name:	Percentage of Residues within binding site
A	55 %
B	45 %

Ligand binding site composition:

B-Factor:	18.648
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.948	1549.125

% Hydrophobic	% Polar
40.96	59.04
According to VolSite

Ligand :

HET Code:	RAP
Formula:	C51H79NO13
Molecular weight:	914.172 g/mol
DrugBank ID:	DB00877
Buried Surface Area:	66.03 %
Polar Surface area:	195.42 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	4
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
35.5057	49.9534	36.0298

Binding mode :

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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
C5	CZ	TYR- 57	3.62	0	Hydrophobic	false
C43	CD1	PHE- 67	4.07	0	Hydrophobic	false
C10	CB	ASP- 68	4.46	0	Hydrophobic	false
O6	OD2	ASP- 68	2.73	172.28	H-Bond (Ligand Donor)	false
O7	NH2	ARG- 73	3.11	135.56	H-Bond (Protein Donor)	false
C44	CD	ARG- 73	4.3	0	Hydrophobic	false
C4	CE2	PHE- 77	3.76	0	Hydrophobic	false
C5	CZ	PHE- 77	3.73	0	Hydrophobic	false
C44	CE1	PHE- 77	4.27	0	Hydrophobic	false
C48	CZ	PHE- 77	3.82	0	Hydrophobic	false
O13	O	GLY- 84	2.66	168.69	H-Bond (Ligand Donor)	false
O10	O	GLN- 85	2.69	159.23	H-Bond (Ligand Donor)	false
C3	CB	VAL- 86	4.23	0	Hydrophobic	false
C4	CG1	VAL- 86	3.84	0	Hydrophobic	false
O2	N	ILE- 87	2.87	146.47	H-Bond (Protein Donor)	false
C3	CG1	ILE- 87	4.25	0	Hydrophobic	false
C42	CG2	ILE- 87	4.19	0	Hydrophobic	false
C5	CZ2	TRP- 90	3.86	0	Hydrophobic	false
C3	CE2	TRP- 90	3.49	0	Hydrophobic	false
O3	OH	TYR- 113	2.65	167.55	H-Bond (Protein Donor)	false
C49	CE1	TYR- 113	3.99	0	Hydrophobic	false
C43	CB	SER- 118	4.38	0	Hydrophobic	false
C43	CD1	ILE- 122	3.46	0	Hydrophobic	false
C3	CZ	PHE- 130	4.48	0	Hydrophobic	false
C45	CB	LEU- 2031	3.79	0	Hydrophobic	false
C24	CG	GLU- 2032	4.31	0	Hydrophobic	false
C45	CG	GLU- 2032	4.47	0	Hydrophobic	false
C47	CB	SER- 2035	4.07	0	Hydrophobic	false
C23	CB	SER- 2035	4.35	0	Hydrophobic	false
C51	CB	ARG- 2036	3.98	0	Hydrophobic	false
C52	CG	ARG- 2036	4.44	0	Hydrophobic	false
C13	CE1	PHE- 2039	4.01	0	Hydrophobic	false
C16	CZ	PHE- 2039	4.31	0	Hydrophobic	false
C36	CB	PHE- 2039	3.81	0	Hydrophobic	false
C38	CB	PHE- 2039	4.3	0	Hydrophobic	false
C47	CD2	PHE- 2039	3.53	0	Hydrophobic	false
C49	CD1	PHE- 2039	3.91	0	Hydrophobic	false
C50	CG2	THR- 2098	3.65	0	Hydrophobic	false
C45	CZ3	TRP- 2101	4.42	0	Hydrophobic	false
C50	CB	TRP- 2101	3.75	0	Hydrophobic	false
C44	CD2	TYR- 2105	3.68	0	Hydrophobic	false
C48	CE1	TYR- 2105	4.15	0	Hydrophobic	false
C23	CD2	PHE- 2108	3.72	0	Hydrophobic	false
C24	CE2	PHE- 2108	4.01	0	Hydrophobic	false
C45	CG	PHE- 2108	3.46	0	Hydrophobic	false
C46	CE2	PHE- 2108	4.01	0	Hydrophobic	false