scPDB - 3k13 entry

Protein Data Bank Entry:

PDB ID : 3k13

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2009-09-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5-methyltetrahydrofolate-homocysteine methyltransferase
ID:	Q8ABD0_BACTN
AC:	Q8ABD0
Organism:	Bacteroides thetaiotaomicron
Reign:	Bacteria
TaxID:	226186
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	28.936
Number of residues:	36
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.998	1245.375

% Hydrophobic	% Polar
33.06	66.94
According to VolSite

Ligand :

HET Code:	THH
Formula:	C20H23N7O6
Molecular weight:	457.440 g/mol
DrugBank ID:	DB11256
Buried Surface Area:	52.69 %
Polar Surface area:	208.69 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
89.4199	29.3325	19.1444

Binding mode :

What is Poseview ?

2D View
3D View

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
N10	O	HOH- 23	2.98	169.51	H-Bond (Ligand Donor)	false
C13	CG	GLU- 358	4.35	0	Hydrophobic	false
C14	CB	GLU- 358	3.92	0	Hydrophobic	false
N	O	GLY- 364	2.99	158.21	H-Bond (Ligand Donor)	false
OE1	N	ARG- 366	3.28	171.83	H-Bond (Protein Donor)	false
OE1	CZ	ARG- 366	3.45	0	Ionic (Protein Cationic)	false
N8	OD2	ASP- 431	2.96	163.26	H-Bond (Ligand Donor)	false
N1	ND2	ASN- 452	3	163.93	H-Bond (Protein Donor)	false
NA2	OD1	ASN- 452	2.84	145.37	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 519	2.66	148.18	H-Bond (Ligand Donor)	false
NA2	OD2	ASP- 519	2.87	136.92	H-Bond (Ligand Donor)	false
C17	CB	SER- 560	3.57	0	Hydrophobic	false
O1	NH2	ARG- 567	2.76	121.55	H-Bond (Protein Donor)	false
O1	CZ	ARG- 567	3.44	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 567	3.42	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 573	3.87	0	Ionic (Protein Cationic)	false
O2	NH1	ARG- 573	2.86	147.01	H-Bond (Protein Donor)	false
O	NH2	ARG- 573	2.87	156.11	H-Bond (Protein Donor)	false
C9	CG2	ILE- 593	4.01	0	Hydrophobic	false
O4	O	HOH- 721	2.62	164.94	H-Bond (Protein Donor)	false