scPDB - 1woo entry

Protein Data Bank Entry:

PDB ID : 1woo

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2004-08-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminomethyltransferase
ID:	GCST_THEMA
AC:	Q9WY54
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	21.927
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.227	243.000

% Hydrophobic	% Polar
51.39	48.61
According to VolSite

Ligand :

HET Code:	THG
Formula:	C19H21N7O6
Molecular weight:	443.413 g/mol
DrugBank ID:	DB02031
Buried Surface Area:	66.39 %
Polar Surface area:	212.92 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	6
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
0.491969	28.5508	14.4862

Binding mode :

What is Poseview ?

2D View
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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
C7	SD	MET- 51	4.41	0	Hydrophobic	false
C9	CE1	TYR- 83	4.06	0	Hydrophobic	false
CB	CB	TYR- 83	4.46	0	Hydrophobic	false
C3'	CE1	TYR- 83	3.49	0	Hydrophobic	false
C5'	CG2	VAL- 98	4.42	0	Hydrophobic	false
N8	O	VAL- 110	2.95	157.5	H-Bond (Ligand Donor)	false
CG	CE2	TYR- 168	3.81	0	Hydrophobic	false
O11	OH	TYR- 169	2.98	165.51	H-Bond (Protein Donor)	false
CB	CE1	TYR- 169	3.85	0	Hydrophobic	false
N3	OE1	GLU- 195	3.12	130.78	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 195	2.84	147.76	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 195	2.66	154.01	H-Bond (Ligand Donor)	false
O4	NH2	ARG- 227	3.31	161.33	H-Bond (Protein Donor)	false
C2'	CB	TYR- 236	3.82	0	Hydrophobic	false
CB	CH2	TRP- 256	3.95	0	Hydrophobic	false
OE1	CZ	ARG- 362	3.23	0	Ionic (Protein Cationic)	false
O4	O	HOH- 2907	2.76	179.96	H-Bond (Protein Donor)	false