scPDB - 2zu8 entry

Protein Data Bank Entry:

PDB ID : 2zu8

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2008-10-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Mannosyl-3-phosphoglycerate synthase
ID:	MPGS_PYRHO
AC:	O58689
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	2.4.1.217

Chains:

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

Ligand binding site composition:

B-Factor:	29.848
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.858	860.625

% Hydrophobic	% Polar
43.14	56.86
According to VolSite

Ligand :

HET Code:	GDD
Formula:	C16H23N5O16P2
Molecular weight:	603.325 g/mol
DrugBank ID:	-
Buried Surface Area:	75.22 %
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
-5.21326	-2.15013	1.88331

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- 58	4.38	0	Hydrophobic	false
O3'	O	PRO- 58	2.89	165.49	H-Bond (Ligand Donor)	false
C2'	CB	LYS- 60	4.42	0	Hydrophobic	false
O2'	OE2	GLU- 62	2.83	159.05	H-Bond (Ligand Donor)	false
C3'	CG	GLU- 62	4.43	0	Hydrophobic	false
N2	O	VAL- 83	2.78	126.32	H-Bond (Ligand Donor)	false
O6	ND2	ASN- 85	3.12	163.76	H-Bond (Protein Donor)	false
N2	OE1	GLN- 117	2.92	133.19	H-Bond (Ligand Donor)	false
N1	OE1	GLN- 117	2.59	147.76	H-Bond (Ligand Donor)	false
O6	N	GLY- 144	3.28	126.6	H-Bond (Protein Donor)	false
C1'	CD	LYS- 145	4.09	0	Hydrophobic	false
C4'	CD	LYS- 145	3.86	0	Hydrophobic	false
O21	OD1	ASP- 168	3.46	129.96	H-Bond (Ligand Donor)	false
O21	OD2	ASP- 168	2.6	176.59	H-Bond (Ligand Donor)	false
C4'	CB	ASP- 168	3.62	0	Hydrophobic	false
O3'	N	ALA- 169	2.95	167.13	H-Bond (Protein Donor)	false
O2B	OD2	ASP- 170	2.89	160.27	H-Bond (Protein Donor)	false
C61	CH2	TRP- 202	3.74	0	Hydrophobic	false
O6A	O	ASN- 248	3.06	172.39	H-Bond (Ligand Donor)	false
O41	O	ASN- 248	2.74	171.35	H-Bond (Ligand Donor)	false
O2A	NZ	LYS- 315	3.63	0	Ionic (Protein Cationic)	false
O3B	NE2	HIS- 319	3.07	161.96	H-Bond (Protein Donor)	false
C21	CE	MET- 323	4.07	0	Hydrophobic	false
C31	SD	MET- 323	4.36	0	Hydrophobic	false
C41	CE	MET- 323	3.97	0	Hydrophobic	false