scPDB - 3rbm entry

Protein Data Bank Entry:

PDB ID : 3rbm

Resolution :2.610 Å

Experimental Method : X-ray

Deposition Date : 2011-03-29

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, putative
ID:	A5K4U6_PLAVS
AC:	A5K4U6
Organism:	Plasmodium vivax
Reign:	Eukaryota
TaxID:	126793
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	84 %
B	16 %

Ligand binding site composition:

B-Factor:	26.275
Number of residues:	47
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	4
Water Molecules:	2
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.147	867.375

% Hydrophobic	% Polar
36.19	63.81
According to VolSite

Ligand :

HET Code:	B73
Formula:	C17H31N2O6P2
Molecular weight:	421.385 g/mol
DrugBank ID:	-
Buried Surface Area:	65.74 %
Polar Surface area:	154.81 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
-36.4283	10.949	-15.8793

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
CAO	CD1	PHE- 122	4.19	0	Hydrophobic	false
CAS	CG	PHE- 122	3.75	0	Hydrophobic	false
CAT	CB	PHE- 122	3.84	0	Hydrophobic	false
CAQ	CD1	PHE- 122	4.14	0	Hydrophobic	false
CAV	CD1	LEU- 123	4.42	0	Hydrophobic	false
CAM	CB	ALA- 125	3.39	0	Hydrophobic	false
CAJ	OD1	ASP- 126	3.68	0	Ionic (Ligand Cationic)	false
CAT	CB	ASP- 126	4.21	0	Hydrophobic	false
OAD	NH2	ARG- 135	2.53	137.27	H-Bond (Protein Donor)	false
OAE	NH2	ARG- 135	3.11	141.05	H-Bond (Protein Donor)	false
OAE	NH1	ARG- 135	2.97	148.28	H-Bond (Protein Donor)	false
OAD	CZ	ARG- 135	3.63	0	Ionic (Protein Cationic)	false
OAE	CZ	ARG- 135	3.48	0	Ionic (Protein Cationic)	false
CAK	CG1	VAL- 153	3.78	0	Hydrophobic	false
CAL	CB	VAL- 153	4.16	0	Hydrophobic	false
CAM	CG1	VAL- 153	3.63	0	Hydrophobic	false
CAK	CG1	VAL- 156	3.29	0	Hydrophobic	false
CAA	CB	LEU- 157	4.45	0	Hydrophobic	false
CAA	CD2	LEU- 157	3.9	0	Hydrophobic	false
CAL	CB	LEU- 157	4.06	0	Hydrophobic	false
CAN	CD1	LEU- 157	3.35	0	Hydrophobic	false
CAQ	CG2	THR- 191	4.41	0	Hydrophobic	false
CAS	CG2	THR- 191	3.57	0	Hydrophobic	false
CAU	CG2	THR- 191	4.27	0	Hydrophobic	false
CAR	CG	GLN- 195	3.57	0	Hydrophobic	false
OAG	NZ	LYS- 243	2.73	148.02	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 243	2.73	0	Ionic (Protein Cationic)	false
CAH	CG	LYS- 243	4.4	0	Hydrophobic	false
CAH	CE2	TYR- 247	4.11	0	Hydrophobic	false
OAB	NZ	LYS- 301	2.89	0	Ionic (Protein Cationic)	false
OAD	NZ	LYS- 301	2.75	0	Ionic (Protein Cationic)	false
OAD	NZ	LYS- 301	2.75	145.65	H-Bond (Protein Donor)	false
OAB	MG	MG- 1001	1.97	0	Metal Acceptor	false
OAC	MG	MG- 1001	2.03	0	Metal Acceptor	false
OAE	MG	MG- 1003	2.11	0	Metal Acceptor	false
OAF	MG	MG- 1003	2.28	0	Metal Acceptor	false