scPDB - 4nke entry

Protein Data Bank Entry:

PDB ID : 4nke

Resolution :1.460 Å

Experimental Method : X-ray

Deposition Date : 2013-11-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.090	8.110	7.800	0.980	9.440	3

List of CHEMBLId :

CHEMBL923

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
A	100 %

Ligand binding site composition:

B-Factor:	10.008
Number of residues:	31
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	4
Water Molecules:	3
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.896	1238.625

% Hydrophobic	% Polar
38.96	61.04
According to VolSite

Ligand :

HET Code:	RIS
Formula:	C7H7NO7P2
Molecular weight:	279.080 g/mol
DrugBank ID:	DB00884
Buried Surface Area:	71.09 %
Polar Surface area:	179.12 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
14.9731	33.0273	-8.17259

Binding mode :

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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
C6	CB	PHE- 99	4.25	0	Hydrophobic	false
C7	CD2	LEU- 100	3.96	0	Hydrophobic	false
C1	CB	ASP- 103	3.76	0	Hydrophobic	false
O12	NH2	ARG- 112	3.12	135.56	H-Bond (Protein Donor)	false
O10	NH1	ARG- 112	2.73	149.49	H-Bond (Protein Donor)	false
O10	NH2	ARG- 112	3.03	134.82	H-Bond (Protein Donor)	false
O10	CZ	ARG- 112	3.3	0	Ionic (Protein Cationic)	false
C6	CG	GLN- 171	4.49	0	Hydrophobic	false
O16	NZ	LYS- 200	2.71	151.08	H-Bond (Protein Donor)	false
O16	NZ	LYS- 200	2.71	0	Ionic (Protein Cationic)	false
N4	OG1	THR- 201	2.92	160.17	H-Bond (Ligand Donor)	false
O13	OD2	ASP- 243	2.93	167.04	H-Bond (Ligand Donor)	false
O11	NZ	LYS- 257	2.82	158.35	H-Bond (Protein Donor)	false
O11	NZ	LYS- 257	2.82	0	Ionic (Protein Cationic)	false
O10	NZ	LYS- 257	3.74	0	Ionic (Protein Cationic)	false
O12	MG	MG- 401	2.07	0	Metal Acceptor	false
O15	MG	MG- 401	2.07	0	Metal Acceptor	false
O11	MG	MG- 402	2	0	Metal Acceptor	false
O17	MG	MG- 402	2.01	0	Metal Acceptor	false
O15	MG	MG- 403	2.03	0	Metal Acceptor	false
O16	O	HOH- 759	2.63	147.75	H-Bond (Protein Donor)	false