scPDB - 1wsv entry

Protein Data Bank Entry:

PDB ID : 1wsv

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2004-11-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminomethyltransferase, mitochondrial
ID:	GCST_HUMAN
AC:	P48728
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.427
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.267	793.125

% Hydrophobic	% Polar
59.57	40.43
According to VolSite

Ligand :

HET Code:	THH
Formula:	C20H23N7O6
Molecular weight:	457.440 g/mol
DrugBank ID:	DB11256
Buried Surface Area:	64.77 %
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
8.5957	16.8641	11.5687

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
C11	SD	MET- 56	4.15	0	Hydrophobic	false
OE2	N	LEU- 88	3.2	159.49	H-Bond (Protein Donor)	false
C9	CD1	LEU- 88	3.84	0	Hydrophobic	false
C13	CD2	LEU- 88	3.56	0	Hydrophobic	false
C16	CD1	LEU- 88	3.58	0	Hydrophobic	false
C9	CB	ASP- 101	4.02	0	Hydrophobic	false
C17	CD1	ILE- 103	3.96	0	Hydrophobic	false
N8	O	VAL- 115	2.71	159.47	H-Bond (Ligand Donor)	false
CG	CE2	PHE- 176	3.55	0	Hydrophobic	false
CG	SD	MET- 177	4.26	0	Hydrophobic	false
C11	CE1	TYR- 197	3.63	0	Hydrophobic	false
N3	OE2	GLU- 204	2.85	159.29	H-Bond (Ligand Donor)	false
NA2	OE2	GLU- 204	3.28	133.89	H-Bond (Ligand Donor)	false
O4	NH2	ARG- 233	3.16	138.22	H-Bond (Protein Donor)	false
C14	CB	LEU- 242	4.37	0	Hydrophobic	false
C13	CD2	LEU- 242	3.92	0	Hydrophobic	false
CB	CH2	TRP- 262	3.43	0	Hydrophobic	false
O2	OH	TYR- 371	2.94	141.33	H-Bond (Protein Donor)	false
O4	O	HOH- 4012	2.67	171.68	H-Bond (Protein Donor)	false