scPDB - 2uyy entry

Protein Data Bank Entry:

PDB ID : 2uyy

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2007-04-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative oxidoreductase GLYR1
ID:	GLYR1_HUMAN
AC:	Q49A26
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1

Chains:

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

Ligand binding site composition:

B-Factor:	39.420
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.502	610.875

% Hydrophobic	% Polar
43.65	56.35
According to VolSite

Ligand :

HET Code:	NA7
Formula:	C15H20N5O16P3
Molecular weight:	619.264 g/mol
DrugBank ID:	-
Buried Surface Area:	64.76 %
Polar Surface area:	358.57 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
32.7694	33.0043	-4.26597

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
O1N	N	MET- 278	2.72	171.99	H-Bond (Protein Donor)	false
C1D	CG	MET- 278	4.49	0	Hydrophobic	false
C5D	CG	MET- 278	4.06	0	Hydrophobic	false
O1X	ND2	ASN- 297	2.83	172.64	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 298	3.43	171.87	H-Bond (Protein Donor)	false
DuAr	CZ	ARG- 298	3.7	152.19	Pi/Cation	false
O2X	N	THR- 299	2.84	127.28	H-Bond (Protein Donor)	false
O2X	OG1	THR- 299	2.94	151.33	H-Bond (Protein Donor)	false
C5D	SG	CYS- 330	3.67	0	Hydrophobic	false
C1B	CG1	VAL- 331	4.18	0	Hydrophobic	false
O3D	O	VAL- 331	3.02	162.68	H-Bond (Ligand Donor)	false
C5B	CB	SER- 332	4.46	0	Hydrophobic	false
N6A	OD2	ASP- 339	3.09	167.94	H-Bond (Ligand Donor)	false
O3D	N	THR- 362	3.13	169.29	H-Bond (Protein Donor)	false
C1D	CB	THR- 362	4.34	0	Hydrophobic	false
C2D	CZ	PHE- 498	3.92	0	Hydrophobic	false
C1D	CE1	PHE- 498	3.8	0	Hydrophobic	false
O3	OH	TYR- 502	2.77	137.55	H-Bond (Protein Donor)	false
C5D	CE2	TYR- 502	4.36	0	Hydrophobic	false
C2D	CD2	TYR- 502	3.75	0	Hydrophobic	false
O1N	O	HOH- 2090	2.63	179.97	H-Bond (Protein Donor)	false