scPDB - 2wvm entry

Protein Data Bank Entry:

PDB ID : 2wvm

Resolution :2.980 Å

Experimental Method : X-ray

Deposition Date : 2009-10-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mannosyl-3-phosphogylcerate synthase
ID:	Q72K30_THET2
AC:	Q72K30
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	262724
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	57.932
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.941	1400.625

% Hydrophobic	% Polar
35.42	64.58
According to VolSite

Ligand :

HET Code:	GDD
Formula:	C16H23N5O16P2
Molecular weight:	603.325 g/mol
DrugBank ID:	-
Buried Surface Area:	61.94 %
Polar Surface area:	352.71 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	8
Rings:	4
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
14.1874	-2.68249	-19.6859

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
C1'	CB	PRO- 60	4.08	0	Hydrophobic	false
C4'	CG	PRO- 60	4.2	0	Hydrophobic	false
O3'	O	PRO- 60	2.65	150.9	H-Bond (Ligand Donor)	false
O2'	N	ARG- 62	3.12	141.61	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 64	2.82	166.19	H-Bond (Ligand Donor)	false
N2	O	ALA- 85	3.4	141.75	H-Bond (Ligand Donor)	false
O6	ND2	ASN- 87	3.09	141.8	H-Bond (Protein Donor)	false
N2	OE1	GLN- 116	3.02	138.2	H-Bond (Ligand Donor)	false
N1	OE1	GLN- 116	2.95	144.37	H-Bond (Ligand Donor)	false
O6	N	GLY- 143	2.77	131.13	H-Bond (Protein Donor)	false
O31	NZ	LYS- 144	3.45	161.8	H-Bond (Protein Donor)	false
C5'	CD	LYS- 144	4.17	0	Hydrophobic	false
O21	OD1	ASP- 167	2.82	174.17	H-Bond (Ligand Donor)	false
O21	OD2	ASP- 167	3.5	123.31	H-Bond (Ligand Donor)	false
C4'	CB	ASP- 167	4.3	0	Hydrophobic	false
O3'	N	ALA- 168	2.97	148.44	H-Bond (Protein Donor)	false
C61	CB	ASN- 248	4.38	0	Hydrophobic	false
O6A	N	GLY- 250	3.02	137.16	H-Bond (Protein Donor)	false
O3B	OH	TYR- 268	2.64	146.08	H-Bond (Protein Donor)	false
C31	CD1	TYR- 268	4.17	0	Hydrophobic	false
O31	OE2	GLU- 271	2.82	145.9	H-Bond (Ligand Donor)	false
O41	OE1	GLU- 271	2.93	149.67	H-Bond (Ligand Donor)	false
O1A	MG	MG- 401	1.99	0	Metal Acceptor	false
O2B	MG	MG- 401	1.89	0	Metal Acceptor	false