scPDB - 4l2x entry

Protein Data Bank Entry:

PDB ID : 4l2x

Resolution :2.550 Å

Experimental Method : X-ray

Deposition Date : 2013-06-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Farnesyl pyrophosphate synthase
ID:	FPPS_HUMAN
AC:	P14324
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.10

Chains:

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

Ligand binding site composition:

B-Factor:	50.225
Number of residues:	41
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	3
Water Molecules:	2
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.583	432.000

% Hydrophobic	% Polar
54.69	45.31
According to VolSite

Ligand :

HET Code:	YL2
Formula:	C16H13N3O6P2S
Molecular weight:	437.303 g/mol
DrugBank ID:	-
Buried Surface Area:	68.12 %
Polar Surface area:	212.05 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
16.327	30.3961	-7.55629

Binding mode :

What is Poseview ?

2D View
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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
CBB	CZ	PHE- 98	3.96	0	Hydrophobic	false
CAP	CB	PHE- 99	3.36	0	Hydrophobic	false
CBB	CD1	PHE- 99	4.06	0	Hydrophobic	false
CBA	CB	ALA- 102	4.16	0	Hydrophobic	false
CAP	CB	ASP- 103	3.51	0	Hydrophobic	false
OAX	CZ	ARG- 112	3.01	0	Ionic (Protein Cationic)	false
OAZ	CZ	ARG- 112	3.6	0	Ionic (Protein Cationic)	false
OAX	NH2	ARG- 112	2.87	126.43	H-Bond (Protein Donor)	false
OAZ	NH2	ARG- 112	2.6	149.18	H-Bond (Protein Donor)	false
SAE	CG2	THR- 167	3.66	0	Hydrophobic	false
CAL	CG2	THR- 167	3.87	0	Hydrophobic	false
CAM	CG	GLU- 168	4.45	0	Hydrophobic	false
CBB	CG	GLU- 168	3.56	0	Hydrophobic	false
CAK	CG	GLN- 171	4.48	0	Hydrophobic	false
CAM	CB	GLN- 171	3.33	0	Hydrophobic	false
CAN	CG	GLN- 171	3.99	0	Hydrophobic	false
OAW	NZ	LYS- 200	3.6	0	Ionic (Protein Cationic)	false
SAE	CB	LYS- 200	4.13	0	Hydrophobic	false
SAE	CE1	TYR- 204	4.41	0	Hydrophobic	false
OAX	NZ	LYS- 257	3.07	167.2	H-Bond (Protein Donor)	false
OAY	NZ	LYS- 257	3.33	123.06	H-Bond (Protein Donor)	false
OAX	NZ	LYS- 257	3.07	0	Ionic (Protein Cationic)	false
OAY	NZ	LYS- 257	3.33	0	Ionic (Protein Cationic)	false
OAV	MG	MG- 403	2.27	0	Metal Acceptor	false
OAZ	MG	MG- 403	2.3	0	Metal Acceptor	false
OAV	MG	MG- 404	2.11	0	Metal Acceptor	false
OAW	MG	MG- 405	2.09	0	Metal Acceptor	false