scPDB - 4f84 entry

Protein Data Bank Entry:

PDB ID : 4f84

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-05-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Geranyl diphosphate 2-C-methyltransferase
ID:	GPPMT_STRLS
AC:	D3KYU3
Organism:	Streptomyces lasaliensis
Reign:	Bacteria
TaxID:	324833
EC Number:	2.1.1.255

Chains:

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

Ligand binding site composition:

B-Factor:	65.891
Number of residues:	21
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.620	263.250

% Hydrophobic	% Polar
60.26	39.74
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	68.8 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
49.6622	49.2547	33.0879

Binding mode :

What is Poseview ?

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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
O3'	N	GLY- 115	3.16	126.88	H-Bond (Protein Donor)	false
C3'	CG2	THR- 135	4.24	0	Hydrophobic	false
C2'	CB	THR- 135	4.45	0	Hydrophobic	false
C1'	CG2	THR- 135	4.46	0	Hydrophobic	false
O2'	N	LEU- 136	3.23	160.73	H-Bond (Protein Donor)	false
N6	OD1	ASN- 163	3.42	157.53	H-Bond (Ligand Donor)	false
N1	N	MET- 164	2.83	168.02	H-Bond (Protein Donor)	false
C4'	CB	SER- 182	4.34	0	Hydrophobic	false
SD	CB	SER- 182	4.18	0	Hydrophobic	false
SD	CE2	TYR- 185	3.42	0	Hydrophobic	false
CE	CZ	TYR- 185	3.57	0	Hydrophobic	false