scPDB - 4dem entry

Protein Data Bank Entry:

PDB ID : 4dem

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2012-01-20

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:	24.096
Number of residues:	39
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	3
Water Molecules:	5
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.217	435.375

% Hydrophobic	% Polar
47.29	52.71
According to VolSite

Ligand :

HET Code:	YS4
Formula:	C15H16N2O7P2
Molecular weight:	398.244 g/mol
DrugBank ID:	-
Buried Surface Area:	66.51 %
Polar Surface area:	180.15 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
16.2818	30.13	-7.21177

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
C3	CZ	PHE- 112	4.02	0	Hydrophobic	false
C2	CD1	PHE- 113	4.29	0	Hydrophobic	false
C8	CB	PHE- 113	3.52	0	Hydrophobic	false
C1	CB	ALA- 116	3.92	0	Hydrophobic	false
N1	OD1	ASP- 117	3.21	124.38	H-Bond (Ligand Donor)	false
C11	CB	ASP- 117	3.72	0	Hydrophobic	false
C8	CB	ASP- 117	3.51	0	Hydrophobic	false
C2	CE	MET- 120	4.19	0	Hydrophobic	false
C1	SD	MET- 120	4.17	0	Hydrophobic	false
O6	CZ	ARG- 126	3.9	0	Ionic (Protein Cationic)	false
O7	CZ	ARG- 126	3.28	0	Ionic (Protein Cationic)	false
O6	NH2	ARG- 126	2.88	137.19	H-Bond (Protein Donor)	false
O7	NH1	ARG- 126	2.73	152.01	H-Bond (Protein Donor)	false
O7	NH2	ARG- 126	2.97	138.7	H-Bond (Protein Donor)	false
C15	CG2	THR- 181	4.3	0	Hydrophobic	false
C6	CG2	THR- 181	3.28	0	Hydrophobic	false
C3	CG	GLU- 182	3.73	0	Hydrophobic	false
C4	CG	GLN- 185	4.12	0	Hydrophobic	false
C1	CG	GLN- 185	4.35	0	Hydrophobic	false
C5	CB	GLN- 185	3.55	0	Hydrophobic	false
O2	NZ	LYS- 214	2.56	161.17	H-Bond (Protein Donor)	false
O2	NZ	LYS- 214	2.56	0	Ionic (Protein Cationic)	false
O4	NZ	LYS- 214	3.77	0	Ionic (Protein Cationic)	false
C15	CB	LYS- 214	4.34	0	Hydrophobic	false
O5	NZ	LYS- 271	2.7	147.27	H-Bond (Protein Donor)	false
O7	NZ	LYS- 271	2.84	120.96	H-Bond (Protein Donor)	false
O5	NZ	LYS- 271	2.7	0	Ionic (Protein Cationic)	false
O7	NZ	LYS- 271	2.84	0	Ionic (Protein Cationic)	false
O3	MG	MG- 402	2.09	0	Metal Acceptor	false
O6	MG	MG- 403	2.13	0	Metal Acceptor	false
O3	MG	MG- 403	2.12	0	Metal Acceptor	false
O5	MG	MG- 404	2.08	0	Metal Acceptor	false
O4	MG	MG- 404	2.08	0	Metal Acceptor	false