scPDB - 3vc1 entry

Protein Data Bank Entry:

PDB ID : 3vc1

Resolution :1.820 Å

Experimental Method : X-ray

Deposition Date : 2012-01-03

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_STRCO
AC:	Q9F1Y5
Organism:	Streptomyces coelicolor / M145)
Reign:	Bacteria
TaxID:	100226
EC Number:	2.1.1.255

Chains:

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

Ligand binding site composition:

B-Factor:	21.994
Number of residues:	43
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	6
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.908	384.750

% Hydrophobic	% Polar
53.51	46.49
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	80.93 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
8.96746	7.46242	-2.938

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
SD	CZ2	TRP- 29	3.76	0	Hydrophobic	false
C3'	CE2	TRP- 29	3.93	0	Hydrophobic	false
SD	CB	HIS- 49	3.74	0	Hydrophobic	false
CB	CB	HIS- 49	3.98	0	Hydrophobic	false
O	N	HIS- 49	2.82	163.39	H-Bond (Protein Donor)	false
N	OD1	ASP- 103	4	0	Ionic (Ligand Cationic)	false
N	O	GLY- 105	2.97	153.16	H-Bond (Ligand Donor)	false
O3'	N	GLY- 107	2.88	127.87	H-Bond (Protein Donor)	false
O2'	OG1	THR- 127	2.95	140.98	H-Bond (Ligand Donor)	false
O2'	N	LEU- 128	3.36	149.9	H-Bond (Protein Donor)	false
O3'	OE1	GLN- 132	2.78	154.65	H-Bond (Ligand Donor)	false
N6	OD1	ASN- 155	3.01	178.51	H-Bond (Ligand Donor)	false
N1	N	MET- 156	2.8	159.62	H-Bond (Protein Donor)	false
N	O	ASN- 172	2.83	165.47	H-Bond (Ligand Donor)	false
C4'	CB	SER- 174	4.07	0	Hydrophobic	false
C5'	CE2	TYR- 177	3.73	0	Hydrophobic	false
O	O	HOH- 443	2.74	156.51	H-Bond (Protein Donor)	false
O	O	HOH- 445	2.68	179.96	H-Bond (Protein Donor)	false
N	O	HOH- 451	2.77	158.92	H-Bond (Ligand Donor)	false