scPDB - 2vmy entry

Protein Data Bank Entry:

PDB ID : 2vmy

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2008-01-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine hydroxymethyltransferase
ID:	Q7SIB6_GEOSE
AC:	Q7SIB6
Organism:	Geobacillus stearothermophilus
Reign:	Bacteria
TaxID:	1422
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	26 %
B	74 %

Ligand binding site composition:

B-Factor:	51.978
Number of residues:	37
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.133	405.000

% Hydrophobic	% Polar
57.50	42.50
According to VolSite

Ligand :

HET Code:	FFO
Formula:	C20H21N7O7
Molecular weight:	471.423 g/mol
DrugBank ID:	DB11596
Buried Surface Area:	67.68 %
Polar Surface area:	221.2 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
26.2428	27.9997	12.8725

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	OE2	GLU- 53	3.23	161.82	H-Bond (Ligand Donor)	false
C9	CB	TYR- 60	4.3	0	Hydrophobic	false
C16	CZ	TYR- 60	3.49	0	Hydrophobic	false
C7	CZ	TYR- 61	4.14	0	Hydrophobic	false
NA2	O	LEU- 117	2.82	121.6	H-Bond (Ligand Donor)	false
C12	CD1	LEU- 117	4.05	0	Hydrophobic	false
NA2	O	GLY- 121	3.09	131.17	H-Bond (Ligand Donor)	false
N3	O	GLY- 121	2.64	150.46	H-Bond (Ligand Donor)	false
O4	N	LEU- 123	2.87	140.1	H-Bond (Protein Donor)	false
C14	CD1	LEU- 123	3.63	0	Hydrophobic	false
C11	CD2	LEU- 123	3.7	0	Hydrophobic	false
O1	NZ	LYS- 248	3.37	124.39	H-Bond (Protein Donor)	false
O2	NZ	LYS- 248	3.16	165.72	H-Bond (Protein Donor)	false
O1	NZ	LYS- 248	3.37	0	Ionic (Protein Cationic)	false
O2	NZ	LYS- 248	3.16	0	Ionic (Protein Cationic)	false
C15	CZ	PHE- 251	3.46	0	Hydrophobic	false
C16	CB	PRO- 252	4.39	0	Hydrophobic	false
N1	ND2	ASN- 341	3.5	134.28	H-Bond (Protein Donor)	false
N8	OD1	ASN- 341	2.59	152.71	H-Bond (Ligand Donor)	false
OE1	OG	SER- 349	3.03	162.45	H-Bond (Protein Donor)	false
CB	CG	PRO- 350	4.27	0	Hydrophobic	false
CG	CB	PRO- 350	3.99	0	Hydrophobic	false
C12	CB	PRO- 350	3.44	0	Hydrophobic	false
OE1	N	GLY- 351	3.28	127.08	H-Bond (Protein Donor)	false