scPDB - 4kbz entry

Protein Data Bank Entry:

PDB ID : 4kbz

Resolution :2.150 Å

Experimental Method : X-ray

Deposition Date : 2013-04-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Egl nine homolog 1
ID:	EGLN1_HUMAN
AC:	Q9GZT9
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:	43.173
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	FE2

Cavity properties

Ligandability	Volume (Å3)
0.244	486.000

% Hydrophobic	% Polar
47.92	52.08
According to VolSite

Ligand :

HET Code:	1QA
Formula:	C19H13N4O4S
Molecular weight:	393.396 g/mol
DrugBank ID:	-
Buried Surface Area:	67.35 %
Polar Surface area:	167.27 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-13.3031	21.7036	-6.74339

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
C23	CG1	VAL- 241	3.59	0	Hydrophobic	false
C24	CB	SER- 242	4.48	0	Hydrophobic	false
C22	CD1	ILE- 256	4.26	0	Hydrophobic	false
S11	CE	MET- 299	3.48	0	Hydrophobic	false
C22	SD	MET- 299	3.76	0	Hydrophobic	false
C12	CZ	TYR- 310	4.28	0	Hydrophobic	false
C12	CB	ASP- 315	4.38	0	Hydrophobic	false
O25	NH1	ARG- 322	3.1	135.74	H-Bond (Protein Donor)	false
O25	NH2	ARG- 322	3.18	133.38	H-Bond (Protein Donor)	false
C1	CD1	ILE- 327	3.7	0	Hydrophobic	false
N28	OH	TYR- 329	2.93	170.17	H-Bond (Protein Donor)	false
C2	CD1	LEU- 343	4.17	0	Hydrophobic	false
C2	CG2	VAL- 376	3.56	0	Hydrophobic	false
N28	NH2	ARG- 383	2.76	139.22	H-Bond (Protein Donor)	false
O17	NZ	LYS- 408	3.12	0	Ionic (Protein Cationic)	false
O18	NZ	LYS- 408	3.02	0	Ionic (Protein Cationic)	false
C21	CB	LYS- 408	4.19	0	Hydrophobic	false
C20	CD	LYS- 408	3.69	0	Hydrophobic	false
O18	NZ	LYS- 408	3.02	165.57	H-Bond (Protein Donor)	false
N4	FE	FE2- 502	2.28	0	Metal Acceptor	false
N8	FE	FE2- 502	2.14	0	Metal Acceptor	false
DuAr	FE	FE2- 502	3.62	80.22	Pi/Cation	false
DuAr	FE	FE2- 502	3.29	79.56	Pi/Cation	false