scPDB - 1av5 entry

Protein Data Bank Entry:

PDB ID : 1av5

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1997-09-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Histidine triad nucleotide-binding protein 1
ID:	HINT1_HUMAN
AC:	P49773
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3

Chains:

Chain Name:	Percentage of Residues within binding site
A	7 %
B	93 %

Ligand binding site composition:

B-Factor:	35.922
Number of residues:	28
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.542	361.125

% Hydrophobic	% Polar
62.62	37.38
According to VolSite

Ligand :

HET Code:	AP2
Formula:	C11H14N5O9P2
Molecular weight:	422.204 g/mol
DrugBank ID:	DB03148
Buried Surface Area:	62.64 %
Polar Surface area:	251.48 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
41.9554	31.1652	53.8211

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
C4'	CZ	PHE- 19	4.49	0	Hydrophobic	false
C1'	CZ	PHE- 19	3.93	0	Hydrophobic	false
O3'	OD2	ASP- 43	2.64	144.44	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 43	2.97	143.01	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 43	2.53	161.76	H-Bond (Ligand Donor)	false
C2'	CB	SER- 45	4.45	0	Hydrophobic	false
C4'	CD1	LEU- 53	4.32	0	Hydrophobic	false
C1'	CD1	LEU- 53	3.86	0	Hydrophobic	false
O1A	ND2	ASN- 99	2.8	167.88	H-Bond (Protein Donor)	false
C3A	CB	SER- 107	3.91	0	Hydrophobic	false
C5'	CG2	VAL- 108	3.97	0	Hydrophobic	false
O1A	NE2	HIS- 114	2.87	166.59	H-Bond (Protein Donor)	false