scPDB - 1yci entry

Protein Data Bank Entry:

PDB ID : 1yci

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2004-12-22

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:	49.595
Number of residues:	23
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
0.921	452.250

% Hydrophobic	% Polar
54.48	45.52
According to VolSite

Ligand :

HET Code:	NDF
Formula:	C11H9NO5
Molecular weight:	235.193 g/mol
DrugBank ID:	DB08263
Buried Surface Area:	71.5 %
Polar Surface area:	109.36 Å2

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

Mass center Coordinates

X	Y	Z
20.3064	25.5742	30.3801

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
CB	CZ	TYR- 145	4.45	0	Hydrophobic	false
CE2	CD2	LEU- 186	3.87	0	Hydrophobic	false
CB	CD1	LEU- 188	3.89	0	Hydrophobic	false
CD2	CD2	LEU- 188	4.04	0	Hydrophobic	false
CD1	CG2	THR- 196	4.05	0	Hydrophobic	false
CB	CG2	THR- 196	4.45	0	Hydrophobic	false
OXT	OG1	THR- 196	2.94	167.22	H-Bond (Protein Donor)	false
O1	ND2	ASN- 205	3.22	127.77	H-Bond (Protein Donor)	false
O	NZ	LYS- 214	2.88	161.99	H-Bond (Protein Donor)	false
O	NZ	LYS- 214	2.88	0	Ionic (Protein Cationic)	false
OXT	NZ	LYS- 214	3.76	0	Ionic (Protein Cationic)	false
O2'	FE	FE2- 1350	2.25	0	Metal Acceptor	false
O2	FE	FE2- 1350	2.24	0	Metal Acceptor	false