scPDB - 2a2d entry

Protein Data Bank Entry:

PDB ID : 2a2d

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2005-06-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-acetylgalactosamine kinase
ID:	GALK2_HUMAN
AC:	Q01415
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.1.157

Chains:

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

Ligand binding site composition:

B-Factor:	24.485
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	MN

Cavity properties

Ligandability	Volume (Å3)
0.904	502.875

% Hydrophobic	% Polar
38.93	61.07
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	74.11 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
13.8576	71.3769	-4.50865

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
O3G	CZ	ARG- 43	3.45	0	Ionic (Protein Cationic)	false
N1	ND2	ASN- 83	2.82	135.28	H-Bond (Protein Donor)	false
C2'	CE2	TYR- 88	4.16	0	Hydrophobic	false
C2'	CB	TRP- 107	4.2	0	Hydrophobic	false
C1'	CD2	TYR- 110	3.81	0	Hydrophobic	false
C4'	CE2	TYR- 110	3.72	0	Hydrophobic	false
C5'	CB	SER- 141	4.06	0	Hydrophobic	false
O2B	N	SER- 142	3.31	145.6	H-Bond (Protein Donor)	false
O3G	OG	SER- 145	2.67	153.87	H-Bond (Protein Donor)	false
O2B	N	SER- 145	3.41	122.49	H-Bond (Protein Donor)	false
O2B	OG	SER- 146	2.79	146.07	H-Bond (Protein Donor)	false
O2B	N	SER- 146	3.35	154.61	H-Bond (Protein Donor)	false
O1B	N	SER- 147	3.03	166.56	H-Bond (Protein Donor)	false
C5'	CB	SER- 147	4.21	0	Hydrophobic	false
C1'	CD2	LEU- 150	4.28	0	Hydrophobic	false
O2G	NZ	LYS- 234	3.29	0	Ionic (Protein Cationic)	false
O1A	N	LYS- 234	3.14	140.98	H-Bond (Protein Donor)	false
O2G	N	ALA- 402	2.95	171.31	H-Bond (Protein Donor)	false
O1G	MN	MN- 460	2.22	0	Metal Acceptor	false
O1B	MN	MN- 460	2.45	0	Metal Acceptor	false
O2A	MN	MN- 460	2.04	0	Metal Acceptor	false
N6	O	HOH- 488	2.78	149.27	H-Bond (Ligand Donor)	false