scPDB - 2msd entry

Protein Data Bank Entry:

PDB ID : 2msd

Resolution : Å

Experimental Method : NMR

Deposition Date : 2014-07-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	MHC class I alpha chain
ID:	A0A024RAV5_H
AC:	A0A024
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	10.000
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.818	455.625

% Hydrophobic	% Polar
49.63	50.37
According to VolSite

Ligand :

HET Code:	GNP
Formula:	C10H13N6O13P3
Molecular weight:	518.164 g/mol
DrugBank ID:	DB02082
Buried Surface Area:	68.6 %
Polar Surface area:	338.36 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
21.0944	-0.100125	42.1884

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
O1B	OG	SER- 17	3.07	167.62	H-Bond (Protein Donor)	false
O1A	N	ALA- 18	2.82	133.83	H-Bond (Protein Donor)	false
C2'	CZ	PHE- 28	3.78	0	Hydrophobic	false
O3'	O	ASP- 30	3.06	131.07	H-Bond (Ligand Donor)	false
C4'	CD1	TYR- 32	3.36	0	Hydrophobic	false
N3B	O	ASP- 33	3.19	136.55	H-Bond (Ligand Donor)	false
O6	ND2	ASN- 116	3.01	128.81	H-Bond (Protein Donor)	false
O6	N	ALA- 146	2.78	122.18	H-Bond (Protein Donor)	false
O6	N	LYS- 147	3.21	133.15	H-Bond (Protein Donor)	false