scPDB - 2p8u entry

Protein Data Bank Entry:

PDB ID : 2p8u

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-03-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hydroxymethylglutaryl-CoA synthase, cytoplasmic
ID:	HMCS1_HUMAN
AC:	Q01581
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.3.3.10

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	30.535
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.163	489.375

% Hydrophobic	% Polar
51.03	48.97
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	49.44 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
45.0393	11.4344	99.5512

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
N6A	O	ALA- 44	3.03	146.13	H-Bond (Ligand Donor)	false
O1A	NZ	LYS- 46	2.75	160.47	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 46	2.75	0	Ionic (Protein Cationic)	false
C5B	CD2	LEU- 51	4.33	0	Hydrophobic	false
CCP	CD2	LEU- 51	4.37	0	Hydrophobic	false
C6P	CZ	TYR- 163	4.4	0	Hydrophobic	false
O4A	ND2	ASN- 167	2.81	173.11	H-Bond (Protein Donor)	false
OAP	O	ASN- 167	2.76	169.58	H-Bond (Ligand Donor)	false
CAP	CB	ALA- 168	4.29	0	Hydrophobic	false
C6P	CG1	VAL- 216	3.81	0	Hydrophobic	false
N4P	OG	SER- 221	3.02	168.1	H-Bond (Ligand Donor)	false
C2P	CB	SER- 221	4.03	0	Hydrophobic	false
CDP	CD1	ILE- 222	4.48	0	Hydrophobic	false
CEP	CD1	ILE- 222	4.35	0	Hydrophobic	false
C2P	CB	TYR- 225	4.11	0	Hydrophobic	false
S1P	CD1	TYR- 225	4.08	0	Hydrophobic	false
S1P	CG	PRO- 266	3.88	0	Hydrophobic	false
CDP	CE2	TYR- 267	3.37	0	Hydrophobic	false
O7A	NZ	LYS- 269	2.74	168.75	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 269	2.74	0	Ionic (Protein Cationic)	false
C2P	CD2	LEU- 270	3.64	0	Hydrophobic	false
O7A	NZ	LYS- 273	3.48	133.42	H-Bond (Protein Donor)	false
O8A	NZ	LYS- 273	2.5	146.54	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 273	3.48	0	Ionic (Protein Cationic)	false
O8A	NZ	LYS- 273	2.5	0	Ionic (Protein Cationic)	false
S1P	CE2	TYR- 375	4.09	0	Hydrophobic	false