scPDB - 3od4 entry

Protein Data Bank Entry:

PDB ID : 3od4

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2010-08-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hypoxia-inducible factor 1-alpha inhibitor
ID:	HIF1N_HUMAN
AC:	Q9NWT6
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.14.11.30

Chains:

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

Ligand binding site composition:

B-Factor:	45.095
Number of residues:	23
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.219	691.875

% Hydrophobic	% Polar
39.02	60.98
According to VolSite

Ligand :

HET Code:	8XQ
Formula:	C10H6NO3
Molecular weight:	188.160 g/mol
DrugBank ID:	-
Buried Surface Area:	76.33 %
Polar Surface area:	73.25 Å2

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

Mass center Coordinates

X	Y	Z
20.2836	25.2619	29.3673

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
CAH	CD2	LEU- 188	3.59	0	Hydrophobic	false
CAL	CD2	LEU- 188	3.78	0	Hydrophobic	false
OAB	OG1	THR- 196	3.06	148.92	H-Bond (Protein Donor)	false
CAH	CG2	THR- 196	3.59	0	Hydrophobic	false
CAM	CG2	THR- 196	3.9	0	Hydrophobic	false
OAA	NZ	LYS- 214	2.81	160.02	H-Bond (Protein Donor)	false
CAF	CD1	ILE- 273	4.39	0	Hydrophobic	false
CAF	CD1	ILE- 281	3.48	0	Hydrophobic	false
CAG	CD1	ILE- 281	3.92	0	Hydrophobic	false
OAC	O	HOH- 389	3.17	142.48	H-Bond (Protein Donor)	false
OAC	ZN	ZN- 1350	2.16	0	Metal Acceptor	false
NAI	ZN	ZN- 1350	2.21	0	Metal Acceptor	false
DuAr	ZN	ZN- 1350	3.5	79.27	Pi/Cation	false
DuAr	ZN	ZN- 1350	3.95	80.73	Pi/Cation	false