scPDB - 2wya entry

Protein Data Bank Entry:

PDB ID : 2wya

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2009-11-13

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, mitochondrial
ID:	HMCS2_HUMAN
AC:	P54868
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.3.3.10

Chains:

Chain Name:	Percentage of Residues within binding site
B	2 %
C	98 %

Ligand binding site composition:

B-Factor:	16.413
Number of residues:	49
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.305	405.000

% Hydrophobic	% Polar
56.67	43.33
According to VolSite

Ligand :

HET Code:	HMG
Formula:	C27H39N7O20P3S
Molecular weight:	906.620 g/mol
DrugBank ID:	DB03169
Buried Surface Area:	57.28 %
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
21.3703	100.72	-29.6403

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- 81	3.25	130.33	H-Bond (Ligand Donor)	false
O4A	NZ	LYS- 83	3.71	0	Ionic (Protein Cationic)	false
C5B	CD2	LEU- 88	4.32	0	Hydrophobic	false
CCP	CD2	LEU- 88	4.47	0	Hydrophobic	false
CDP	CD2	LEU- 88	4.45	0	Hydrophobic	false
O4	N	CYS- 166	3.16	145.22	H-Bond (Protein Donor)	false
C4	SG	CYS- 166	3.71	0	Hydrophobic	false
O5A	ND2	ASN- 204	2.83	164.74	H-Bond (Protein Donor)	false
OAP	O	ASN- 204	2.71	169.55	H-Bond (Ligand Donor)	false
CAP	CB	ALA- 205	4.45	0	Hydrophobic	false
N8P	OG1	THR- 208	3.25	125.72	H-Bond (Ligand Donor)	false
C4	CE1	PHE- 241	3.57	0	Hydrophobic	false
C6	CD1	PHE- 241	4.12	0	Hydrophobic	false
C6P	CG2	VAL- 253	3.82	0	Hydrophobic	false
N4P	OG	SER- 258	2.86	166.9	H-Bond (Ligand Donor)	false
S1P	CB	SER- 258	3.56	0	Hydrophobic	false
CDP	CD1	ILE- 259	4.26	0	Hydrophobic	false
CEP	CD1	ILE- 259	4.2	0	Hydrophobic	false
C2P	CG1	ILE- 259	4.22	0	Hydrophobic	false
C2P	CB	TYR- 262	4.11	0	Hydrophobic	false
O7	NE2	HIS- 301	2.93	148.15	H-Bond (Protein Donor)	false
C2P	CG	PRO- 303	4.06	0	Hydrophobic	false
CDP	CE2	PHE- 304	3.4	0	Hydrophobic	false
O9A	NZ	LYS- 306	3.91	0	Ionic (Protein Cationic)	false
C2P	SD	MET- 307	4.46	0	Hydrophobic	false
O7A	NZ	LYS- 310	2.92	123.56	H-Bond (Protein Donor)	false
O9A	NZ	LYS- 310	2.59	155.79	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 310	2.92	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 310	2.59	0	Ionic (Protein Cationic)	false
O7	ND2	ASN- 380	3.11	168.54	H-Bond (Protein Donor)	false
C4	CE1	TYR- 382	4.1	0	Hydrophobic	false
S1P	CE2	TYR- 412	4.03	0	Hydrophobic	false
C2	CD2	TYR- 412	3.86	0	Hydrophobic	false
C4	CB	SER- 414	4.44	0	Hydrophobic	false
O4	N	SER- 414	2.84	174.14	H-Bond (Protein Donor)	false