scPDB - 5bp7 entry

Protein Data Bank Entry:

PDB ID : 5bp7

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2015-05-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	SAM-dependent methyltransferase
ID:	Q74AD5_GEOSL
AC:	Q74AD5
Organism:	Geobacter sulfurreducens
Reign:	Bacteria
TaxID:	243231
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.332
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.116	860.625

% Hydrophobic	% Polar
55.69	44.31
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	70.16 %
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
35.9162	18.4171	35.7392

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
C2'	CG2	ILE- 4	3.83	0	Hydrophobic	false
SD	CB	HIS- 18	3.72	0	Hydrophobic	false
CB	CB	HIS- 18	3.84	0	Hydrophobic	false
OXT	N	HIS- 18	2.67	162.72	H-Bond (Protein Donor)	false
O	ND2	ASN- 19	2.67	124.61	H-Bond (Protein Donor)	false
N	O	GLY- 45	2.86	156.15	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 67	3.31	122.57	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 67	2.8	173.86	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 67	2.69	156.49	H-Bond (Ligand Donor)	false
N3	N	MET- 68	3.25	143.46	H-Bond (Protein Donor)	false
N6	OD1	ASP- 95	2.91	159.82	H-Bond (Ligand Donor)	false
N1	N	ALA- 96	2.85	175.68	H-Bond (Protein Donor)	false
N	O	VAL- 111	2.89	152.82	H-Bond (Ligand Donor)	false
C5'	CB	ALA- 113	4.1	0	Hydrophobic	false
C5'	CH2	TRP- 115	4.13	0	Hydrophobic	false
N7	NE1	TRP- 115	3.14	169.25	H-Bond (Protein Donor)	false
OXT	O	HOH- 424	2.93	176.4	H-Bond (Protein Donor)	false