scPDB - 2r4f entry

Protein Data Bank Entry:

PDB ID : 2r4f

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2007-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-hydroxy-3-methylglutaryl-coenzyme A reductase
ID:	HMDH_HUMAN
AC:	P04035
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.34

Chains:

Chain Name:	Percentage of Residues within binding site
C	53 %
D	47 %

Ligand binding site composition:

B-Factor:	18.105
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.539	702.000

% Hydrophobic	% Polar
38.46	61.54
According to VolSite

Ligand :

HET Code:	RIE
Formula:	C29H35FN3O5
Molecular weight:	524.604 g/mol
DrugBank ID:	-
Buried Surface Area:	61.9 %
Polar Surface area:	118.72 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
58.2699	-17.4377	32.8243

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
O4	OE2	GLU- 559	2.54	154.53	H-Bond (Ligand Donor)	false
C12	CB	CYS- 561	3.79	0	Hydrophobic	false
C20	CB	CYS- 561	3.74	0	Hydrophobic	false
C13	CD1	LEU- 562	4.29	0	Hydrophobic	false
C12	CB	LEU- 562	4.29	0	Hydrophobic	false
C29	CB	ALA- 564	3.51	0	Hydrophobic	false
O2	OG	SER- 565	2.7	161.66	H-Bond (Protein Donor)	false
C13	CB	SER- 565	3.94	0	Hydrophobic	false
C32	CB	SER- 565	4	0	Hydrophobic	false
C26	CD	ARG- 568	4.17	0	Hydrophobic	false
F1	CD	ARG- 590	4.29	0	Hydrophobic	false
O3	NH2	ARG- 590	3.04	150.56	H-Bond (Protein Donor)	false
O3	NH1	ARG- 590	3.15	144.17	H-Bond (Protein Donor)	false
F1	CB	SER- 661	3.33	0	Hydrophobic	false
F1	CG1	VAL- 683	3.42	0	Hydrophobic	false
O6	OG	SER- 684	3.32	154.42	H-Bond (Protein Donor)	false
O7	OG	SER- 684	2.58	139.79	H-Bond (Protein Donor)	false
O3	OD2	ASP- 690	2.7	161.45	H-Bond (Ligand Donor)	false
C35	CB	ASP- 690	4.36	0	Hydrophobic	false
C10	CD	LYS- 691	4.24	0	Hydrophobic	false
O4	NZ	LYS- 691	2.95	158.99	H-Bond (Protein Donor)	false
O7	NZ	LYS- 692	3.05	0	Ionic (Protein Cationic)	false
O6	NZ	LYS- 735	2.76	176.19	H-Bond (Protein Donor)	false
O7	NZ	LYS- 735	3.38	124.29	H-Bond (Protein Donor)	false
O6	NZ	LYS- 735	2.76	0	Ionic (Protein Cationic)	false
O7	NZ	LYS- 735	3.38	0	Ionic (Protein Cationic)	false
C10	CB	HIS- 752	4.1	0	Hydrophobic	false
C35	CB	HIS- 752	4.22	0	Hydrophobic	false
O4	ND2	ASN- 755	2.89	160.81	H-Bond (Protein Donor)	false
C8	CD1	LEU- 853	4.19	0	Hydrophobic	false
C13	CD1	LEU- 853	4.2	0	Hydrophobic	false
C21	CD1	LEU- 853	3.81	0	Hydrophobic	false
C35	CD2	LEU- 853	4.09	0	Hydrophobic	false
C16	CB	ALA- 856	3.78	0	Hydrophobic	false
C24	CD2	LEU- 857	3.97	0	Hydrophobic	false