scPDB - 2gcg entry

Protein Data Bank Entry:

PDB ID : 2gcg

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2006-03-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glyoxylate reductase/hydroxypyruvate reductase
ID:	GRHPR_HUMAN
AC:	Q9UBQ7
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.79

Chains:

Chain Name:	Percentage of Residues within binding site
C	2 %
D	98 %

Ligand binding site composition:

B-Factor:	34.740
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.710	556.875

% Hydrophobic	% Polar
39.39	60.61
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	60.51 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-10.4187	-21.812	-57.2658

Binding mode :

What is Poseview ?

2D View
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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
C5N	CB	VAL- 83	4.27	0	Hydrophobic	false
C3D	CG1	VAL- 83	3.69	0	Hydrophobic	false
C5N	CG	LEU- 107	4.24	0	Hydrophobic	false
C4N	CG2	THR- 111	3.6	0	Hydrophobic	false
O1A	N	ARG- 163	2.59	133.02	H-Bond (Protein Donor)	false
O1N	N	ILE- 164	2.98	157.11	H-Bond (Protein Donor)	false
C5N	CD1	ILE- 164	3.64	0	Hydrophobic	false
C5D	CD1	ILE- 164	3.47	0	Hydrophobic	false
N7A	NE	ARG- 185	3.32	136.22	H-Bond (Protein Donor)	false
O2X	NE	ARG- 185	2.58	121.67	H-Bond (Protein Donor)	false
O3X	N	ARG- 185	3.2	145.28	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 185	2.93	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 188	2.98	169.56	H-Bond (Protein Donor)	false
C4B	CB	CYS- 216	4.45	0	Hydrophobic	false
C1B	CB	CYS- 216	3.72	0	Hydrophobic	false
C5B	CB	SER- 217	4.5	0	Hydrophobic	false
O4B	N	SER- 217	3.03	152.38	H-Bond (Protein Donor)	false
O3D	OG	SER- 217	3.28	148.52	H-Bond (Protein Donor)	false
N7N	O	ILE- 243	3.29	154.99	H-Bond (Ligand Donor)	false
N7N	OD2	ASP- 269	2.6	165.84	H-Bond (Ligand Donor)	false
O7N	O	HOH- 2014	2.51	179.97	H-Bond (Protein Donor)	false