scPDB - 3iid entry

Protein Data Bank Entry:

PDB ID : 3iid

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2009-07-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Core histone macro-H2A.1
ID:	H2AY_HUMAN
AC:	O75367
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	40.031
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.606	418.500

% Hydrophobic	% Polar
52.42	47.58
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	78.83 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
11.8421	-36.6938	-1.39444

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
N6	OD1	ASP- 203	2.69	162.65	H-Bond (Ligand Donor)	false
N1	N	ILE- 204	3.04	174.96	H-Bond (Protein Donor)	false
C5D	CB	PRO- 215	4.1	0	Hydrophobic	false
C2D	CB	ASN- 217	3.87	0	Hydrophobic	false
O1D	O	TYR- 221	3.22	134.92	H-Bond (Ligand Donor)	false
C1D	CD2	TYR- 221	4.23	0	Hydrophobic	false
O1D	N	GLY- 224	3.24	127.42	H-Bond (Protein Donor)	false
O2A	N	GLU- 225	2.95	164.03	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 226	4.38	0	Hydrophobic	false
C5'	CG2	VAL- 226	4.36	0	Hydrophobic	false
O1A	N	VAL- 226	2.71	171.27	H-Bond (Protein Donor)	false
O1B	OG	SER- 275	2.59	171.38	H-Bond (Protein Donor)	false
C4'	CB	SER- 310	4.3	0	Hydrophobic	false
O1B	N	GLY- 312	2.79	140.32	H-Bond (Protein Donor)	false
O3'	OG	SER- 313	2.57	155.05	H-Bond (Ligand Donor)	false
O2B	N	GLY- 314	2.83	142.12	H-Bond (Protein Donor)	false
O2A	N	ARG- 315	2.94	174.96	H-Bond (Protein Donor)	false
C4D	CB	ARG- 315	3.66	0	Hydrophobic	false
O2B	N	ASN- 316	3.03	158	H-Bond (Protein Donor)	false
O3D	OD1	ASN- 316	2.63	159.66	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 352	2.55	135.96	H-Bond (Ligand Donor)	false
N3	O	HOH- 506	2.89	161.39	H-Bond (Protein Donor)	false
O1A	O	HOH- 510	2.6	147.85	H-Bond (Protein Donor)	false
O1D	O	HOH- 534	2.72	142.6	H-Bond (Protein Donor)	false