scPDB - 3cd5 entry

Protein Data Bank Entry:

PDB ID : 3cd5

Resolution :2.390 Å

Experimental Method : X-ray

Deposition Date : 2008-02-26

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	62 %
D	38 %

Ligand binding site composition:

B-Factor:	35.030
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.790	513.000

% Hydrophobic	% Polar
54.61	45.39
According to VolSite

Ligand :

HET Code:	7HI
Formula:	C31H37N2O5
Molecular weight:	517.636 g/mol
DrugBank ID:	-
Buried Surface Area:	59.51 %
Polar Surface area:	114.62 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
30.7049	-16.6933	11.7262

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	2.53	129.38	H-Bond (Ligand Donor)	false
C6	CB	CYS- 561	4.47	0	Hydrophobic	false
C26	CB	CYS- 561	3.75	0	Hydrophobic	false
C13	CD1	LEU- 562	4.09	0	Hydrophobic	false
C18	CB	ALA- 564	4.16	0	Hydrophobic	false
C26	CB	SER- 565	4.46	0	Hydrophobic	false
C17	CB	SER- 565	3.64	0	Hydrophobic	false
O2	OG	SER- 565	2.73	153.15	H-Bond (Protein Donor)	false
C20	CD	ARG- 568	4.45	0	Hydrophobic	false
C24	CB	ARG- 568	4.48	0	Hydrophobic	false
C15	CD	ARG- 568	3.54	0	Hydrophobic	false
O3	NH2	ARG- 590	3.34	126.58	H-Bond (Protein Donor)	false
O3	NH1	ARG- 590	2.87	141.45	H-Bond (Protein Donor)	false
O6	OG	SER- 684	3.36	129.38	H-Bond (Protein Donor)	false
C35	CB	ASP- 690	4.03	0	Hydrophobic	false
C10	CD	LYS- 691	4.27	0	Hydrophobic	false
O4	NZ	LYS- 691	2.78	147.41	H-Bond (Protein Donor)	false
O7	NZ	LYS- 692	3.07	121.55	H-Bond (Protein Donor)	false
O7	NZ	LYS- 692	3.07	0	Ionic (Protein Cationic)	false
O6	NZ	LYS- 692	3.81	0	Ionic (Protein Cationic)	false
O7	NZ	LYS- 735	3.29	131.22	H-Bond (Protein Donor)	false
O6	NZ	LYS- 735	2.8	169.63	H-Bond (Protein Donor)	false
O7	NZ	LYS- 735	3.29	0	Ionic (Protein Cationic)	false
O6	NZ	LYS- 735	2.8	0	Ionic (Protein Cationic)	false
C10	CB	HIS- 752	4.01	0	Hydrophobic	false
C35	CB	HIS- 752	4.25	0	Hydrophobic	false
O4	ND2	ASN- 755	3.1	157.76	H-Bond (Protein Donor)	false
C8	CD2	LEU- 853	4.17	0	Hydrophobic	false
C13	CD1	LEU- 853	4.43	0	Hydrophobic	false
C27	CD1	LEU- 853	4.43	0	Hydrophobic	false
C14	CD1	LEU- 853	3.99	0	Hydrophobic	false
C11	CD2	LEU- 853	4.47	0	Hydrophobic	false
C17	CB	ALA- 856	4.39	0	Hydrophobic	false
C14	CB	ALA- 856	4.01	0	Hydrophobic	false
C7	CD	LYS- 864	3.71	0	Hydrophobic	false
C14	CB	LYS- 864	4.1	0	Hydrophobic	false
C27	CB	LYS- 864	3.94	0	Hydrophobic	false