scPDB - 1dq9 entry

Protein Data Bank Entry:

PDB ID : 1dq9

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 1999-12-30

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	36 %
D	64 %

Ligand binding site composition:

B-Factor:	44.819
Number of residues:	53
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.306	624.375

% Hydrophobic	% Polar
37.30	62.70
According to VolSite

Ligand :

HET Code:	HMG
Formula:	C27H39N7O20P3S
Molecular weight:	906.620 g/mol
DrugBank ID:	DB03169
Buried Surface Area:	59.41 %
Polar Surface area:	490.04 Å2

Number of
H-Bond Acceptors:	25
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	24

Mass center Coordinates

X	Y	Z
23.5597	-32.7501	35.742

Binding mode :

What is Poseview ?

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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
C3B	CZ	TYR- 479	3.97	0	Hydrophobic	false
C2B	CE2	TYR- 479	3.8	0	Hydrophobic	false
C2P	CG	GLU- 559	4.29	0	Hydrophobic	false
C6P	CB	CYS- 561	4.02	0	Hydrophobic	false
CEP	CB	ALA- 564	3.96	0	Hydrophobic	false
CEP	CB	SER- 565	4.47	0	Hydrophobic	false
C6P	CB	SER- 565	3.34	0	Hydrophobic	false
N3A	ND2	ASN- 567	3.06	158.66	H-Bond (Protein Donor)	false
O4A	CZ	ARG- 568	3.81	0	Ionic (Protein Cationic)	false
O4A	NE	ARG- 568	3.21	153.81	H-Bond (Protein Donor)	false
C4B	CG	ARG- 568	4.25	0	Hydrophobic	false
CEP	CB	ARG- 568	4.12	0	Hydrophobic	false
CAP	CD	ARG- 568	4.44	0	Hydrophobic	false
C1B	CB	ARG- 568	3.64	0	Hydrophobic	false
O7A	NE	ARG- 571	2.9	129.62	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 571	3.29	122.13	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 571	3.46	0	Ionic (Protein Cationic)	false
O7	NH2	ARG- 590	2.99	157.59	H-Bond (Protein Donor)	false
O7	NH1	ARG- 590	3.25	142.3	H-Bond (Protein Donor)	false
O4	NH1	ARG- 590	3.21	131.96	H-Bond (Protein Donor)	false
O3	OG	SER- 684	3.18	131.59	H-Bond (Protein Donor)	false
O4	OG	SER- 684	2.58	148.05	H-Bond (Protein Donor)	false
O7	OD2	ASP- 690	2.92	164.05	H-Bond (Ligand Donor)	false
C4	CB	ASP- 690	4.42	0	Hydrophobic	false
C2	CD	LYS- 691	4.46	0	Hydrophobic	false
O3	NZ	LYS- 692	3.82	0	Ionic (Protein Cationic)	false
O4	NZ	LYS- 692	3.27	0	Ionic (Protein Cationic)	false
O4A	NZ	LYS- 722	3	148.3	H-Bond (Protein Donor)	false
O4A	NZ	LYS- 722	3	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 722	3.07	0	Ionic (Protein Cationic)	false
O3	NZ	LYS- 735	2.78	154.11	H-Bond (Protein Donor)	false
O3	NZ	LYS- 735	2.78	0	Ionic (Protein Cationic)	false
C2	CB	HIS- 752	4.36	0	Hydrophobic	false
C4	CB	HIS- 752	4.22	0	Hydrophobic	false
C4	CD2	LEU- 853	4.13	0	Hydrophobic	false
C6	CD2	LEU- 853	4.21	0	Hydrophobic	false
S1P	CD1	LEU- 862	4.2	0	Hydrophobic	false
C6	CD2	LEU- 862	3.64	0	Hydrophobic	false
CDP	CB	SER- 865	3.92	0	Hydrophobic	false