scPDB - 2q6b entry

Protein Data Bank Entry:

PDB ID : 2q6b

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-06-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.670	7.670	7.670	0.000	7.670	1

List of CHEMBLId :

CHEMBL521039

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
A	57 %
B	43 %

Ligand binding site composition:

B-Factor:	26.816
Number of residues:	44
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.131	749.250

% Hydrophobic	% Polar
39.19	60.81
According to VolSite

Ligand :

HET Code:	HR2
Formula:	C30H34FN2O5
Molecular weight:	521.600 g/mol
DrugBank ID:	-
Buried Surface Area:	69.51 %
Polar Surface area:	105.83 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
17.0192	15.9964	17.2841

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
O33	OE2	GLU- 559	2.78	148.77	H-Bond (Ligand Donor)	false
C12	CG	GLU- 559	4.45	0	Hydrophobic	false
C28	CB	CYS- 561	4.06	0	Hydrophobic	false
C12	CB	CYS- 561	3.56	0	Hydrophobic	false
C12	CB	LEU- 562	4.23	0	Hydrophobic	false
C11	CD1	LEU- 562	4.03	0	Hydrophobic	false
C11	CB	SER- 565	4.45	0	Hydrophobic	false
C28	CB	SER- 565	3.45	0	Hydrophobic	false
O14	OG	SER- 565	2.71	150.89	H-Bond (Protein Donor)	false
C30	CD	ARG- 568	4.26	0	Hydrophobic	false
O34	NH1	ARG- 590	3.34	140.3	H-Bond (Protein Donor)	false
O34	NH2	ARG- 590	3.03	157.64	H-Bond (Protein Donor)	false
F1	CB	SER- 661	3.56	0	Hydrophobic	false
F1	CG2	VAL- 683	3.51	0	Hydrophobic	false
C7	CG1	VAL- 683	3.63	0	Hydrophobic	false
O27	OG	SER- 684	3.3	159.71	H-Bond (Protein Donor)	false
O26	OG	SER- 684	2.56	135.26	H-Bond (Protein Donor)	false
C24	CB	ASP- 690	4.25	0	Hydrophobic	false
O34	OD2	ASP- 690	2.78	155.34	H-Bond (Ligand Donor)	false
C22	CD	LYS- 691	4.18	0	Hydrophobic	false
O33	NZ	LYS- 691	2.79	163.27	H-Bond (Protein Donor)	false
O26	NZ	LYS- 692	3.03	0	Ionic (Protein Cationic)	false
O27	NZ	LYS- 735	2.68	175.07	H-Bond (Protein Donor)	false
O26	NZ	LYS- 735	3.29	120.53	H-Bond (Protein Donor)	false
O27	NZ	LYS- 735	2.68	0	Ionic (Protein Cationic)	false
O26	NZ	LYS- 735	3.29	0	Ionic (Protein Cationic)	false
C22	CB	HIS- 752	4.12	0	Hydrophobic	false
C24	CB	HIS- 752	4.36	0	Hydrophobic	false
O33	ND2	ASN- 755	3.1	169.72	H-Bond (Protein Donor)	false
C6	CD1	LEU- 853	4.04	0	Hydrophobic	false
C20	CD2	LEU- 853	4.14	0	Hydrophobic	false
C11	CD1	LEU- 853	4.21	0	Hydrophobic	false
C23	CD2	LEU- 853	4.46	0	Hydrophobic	false
C14	CD1	LEU- 853	4.14	0	Hydrophobic	false
C6	CB	ALA- 856	4.04	0	Hydrophobic	false
C32	CB	ALA- 856	3.79	0	Hydrophobic	false
C18	CD2	LEU- 857	4.17	0	Hydrophobic	false
C6	CD2	LEU- 862	4.47	0	Hydrophobic	false
C7	CD2	LEU- 862	4.24	0	Hydrophobic	false
C15	CB	LEU- 862	4.1	0	Hydrophobic	false
O26	O	HOH- 3012	2.59	179.94	H-Bond (Protein Donor)	false