scPDB - 3mp3 entry

Protein Data Bank Entry:

PDB ID : 3mp3

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2010-04-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hydroxymethylglutaryl-CoA lyase, mitochondrial
ID:	HMGCL_HUMAN
AC:	P35914
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	4.1.3.4

Chains:

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

Ligand binding site composition:

B-Factor:	36.805
Number of residues:	48
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.405	462.375

% Hydrophobic	% Polar
37.23	62.77
According to VolSite

Ligand :

HET Code:	HGG
Formula:	C26H37N7O20P3S
Molecular weight:	892.593 g/mol
DrugBank ID:	-
Buried Surface Area:	52.05 %
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
20.0628	-26.0181	-5.13953

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
O1'	NH1	ARG- 41	3.25	164.43	H-Bond (Protein Donor)	false
O3'	NH2	ARG- 41	3.03	168.04	H-Bond (Protein Donor)	false
O1'	NE2	GLN- 45	3.1	135.87	H-Bond (Protein Donor)	false
C61	CG1	VAL- 77	3.34	0	Hydrophobic	false
C15	CB	SER- 78	4.24	0	Hydrophobic	false
O36	NE1	TRP- 81	3.41	143.89	H-Bond (Protein Donor)	false
C46	CZ2	TRP- 81	3.61	0	Hydrophobic	false
C61	CB	TRP- 81	4.42	0	Hydrophobic	false
C61	CG1	VAL- 82	4.32	0	Hydrophobic	false
C73	CD2	LEU- 106	3.82	0	Hydrophobic	false
O20	NZ	LYS- 111	3.45	135.2	H-Bond (Protein Donor)	false
C61	CZ	PHE- 127	4.38	0	Hydrophobic	false
C73	CE2	PHE- 127	4.36	0	Hydrophobic	false
S81	CD2	PHE- 127	3.89	0	Hydrophobic	false
C46	CB	ASN- 140	3.65	0	Hydrophobic	false
C3'	CG	TYR- 167	4.04	0	Hydrophobic	false
C4'	CD1	TYR- 167	3.61	0	Hydrophobic	false
O4'	OG	SER- 169	2.59	153.58	H-Bond (Protein Donor)	false
O4'	OG1	THR- 205	2.7	165.21	H-Bond (Protein Donor)	false
O5'	MG	MG- 401	2.5	0	Metal Acceptor	false