scPDB - 4nka entry

Protein Data Bank Entry:

PDB ID : 4nka

Resolution :2.190 Å

Experimental Method : X-ray

Deposition Date : 2013-11-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.350	6.430	6.430	0.080	6.510	2

List of CHEMBLId :

CHEMBL3109570

Binding Site :

Uniprot Annotation

Name:	Fibroblast growth factor receptor 1
ID:	FGFR1_HUMAN
AC:	P11362
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	62.190
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.421	783.000

% Hydrophobic	% Polar
56.90	43.10
According to VolSite

Ligand :

HET Code:	2K7
Formula:	C22H25N7O3
Molecular weight:	435.479 g/mol
DrugBank ID:	-
Buried Surface Area:	58.54 %
Polar Surface area:	123.01 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
28.9159	2.25388	21.4795

Binding mode :

What is Poseview ?

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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
C7	CD2	LEU- 484	4.27	0	Hydrophobic	false
C4	CB	LEU- 484	3.9	0	Hydrophobic	false
C12	CG1	VAL- 492	4.12	0	Hydrophobic	false
C19	CG2	VAL- 492	4.3	0	Hydrophobic	false
C20	CG2	VAL- 492	4.38	0	Hydrophobic	false
C4	CB	VAL- 492	4.39	0	Hydrophobic	false
C12	CB	ALA- 512	3.82	0	Hydrophobic	false
C20	CD	LYS- 514	4.13	0	Hydrophobic	false
C21	CD	LYS- 514	3.67	0	Hydrophobic	false
C18	CD	LYS- 514	3.8	0	Hydrophobic	false
O2	NZ	LYS- 514	3.38	121.08	H-Bond (Protein Donor)	false
O1	NZ	LYS- 514	2.74	157.33	H-Bond (Protein Donor)	false
C21	CB	GLU- 531	3.87	0	Hydrophobic	false
C21	SD	MET- 535	4.17	0	Hydrophobic	false
C15	CG2	ILE- 545	3.8	0	Hydrophobic	false
C13	CG2	ILE- 545	4.35	0	Hydrophobic	false
C12	CG2	VAL- 561	3.67	0	Hydrophobic	false
C15	CG2	VAL- 561	4.02	0	Hydrophobic	false
N5	O	GLU- 562	2.81	146.8	H-Bond (Ligand Donor)	false
N6	N	ALA- 564	2.89	165.34	H-Bond (Protein Donor)	false
N4	O	ALA- 564	2.87	155.25	H-Bond (Ligand Donor)	false
C7	CD2	LEU- 630	4.48	0	Hydrophobic	false
C	CD2	LEU- 630	4.47	0	Hydrophobic	false
C13	CD1	LEU- 630	3.72	0	Hydrophobic	false
C	CB	ALA- 640	4.1	0	Hydrophobic	false
C13	CB	ALA- 640	3.92	0	Hydrophobic	false