scPDB - 2yd0 entry

Protein Data Bank Entry:

PDB ID : 2yd0

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2011-03-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Endoplasmic reticulum aminopeptidase 1
ID:	ERAP1_HUMAN
AC:	Q9NZ08
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.11

Chains:

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

Ligand binding site composition:

B-Factor:	15.169
Number of residues:	31
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.160	610.875

% Hydrophobic	% Polar
28.18	71.82
According to VolSite

Ligand :

HET Code:	BES
Formula:	C16H24N2O4
Molecular weight:	308.373 g/mol
DrugBank ID:	DB03424
Buried Surface Area:	64.63 %
Polar Surface area:	117.1 Å2

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

Mass center Coordinates

X	Y	Z
9.04564	73.4381	23.4837

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
N2	OE2	GLU- 183	3.53	0	Ionic (Ligand Cationic)	false
C12	CB	GLU- 183	3.69	0	Hydrophobic	false
C8	CB	SER- 316	3.79	0	Hydrophobic	false
O1	N	GLY- 317	2.99	143.46	H-Bond (Protein Donor)	false
N1	O	ALA- 318	3.06	156.1	H-Bond (Ligand Donor)	false
O1	N	ALA- 318	3.22	164.8	H-Bond (Protein Donor)	false
C6	SD	MET- 319	3.28	0	Hydrophobic	false
N2	OE2	GLU- 320	2.96	123.49	H-Bond (Ligand Donor)	false
N2	OE1	GLU- 320	2.51	169.13	H-Bond (Ligand Donor)	false
O2	OE1	GLU- 320	2.82	138.22	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 320	2.96	0	Ionic (Ligand Cationic)	false
N2	OE1	GLU- 320	2.51	0	Ionic (Ligand Cationic)	false
C15	CB	HIS- 353	4.18	0	Hydrophobic	false
N2	OE2	GLU- 376	2.74	152.77	H-Bond (Ligand Donor)	false
N2	OE2	GLU- 376	2.74	0	Ionic (Ligand Cationic)	false
O3	OH	TYR- 438	2.64	149.48	H-Bond (Protein Donor)	false
C16	CE2	TYR- 438	3.49	0	Hydrophobic	false
O2	ZN	ZN- 1946	1.86	0	Metal Acceptor	false
O3	ZN	ZN- 1946	1.92	0	Metal Acceptor	false
N2	O	HOH- 2056	3.11	125.84	H-Bond (Ligand Donor)	false