Inhibitor SU 5402 in Tyrosine Kinase Domain of FGFR 1: Kinemages

Inhibitor SU-5402 Bound to the Tyrosine Kinase Domain of FGFR 1

Larry P. Taylor, Ph. D.

Feedback appreciated; please send comments to:

Email: lpt

Molecular & Behavioral Neuroscience Institute

The University of Michigan

Ann Arbor, MI

FGF molecules function by interacting with FGF receptors. These receptors typically contain Ig-like binding domains (with domains D2 and D3 being most involved in FGF-FGF receptor interactions), a short transmembrane spanning domain and a cytoplasmic component that possesses tyrosine kinase activity. An essential component of biological activity is the heparin-mediated dimerization of the FGF receptor.

Most FGF receptors contain a tyrosine kinase motif downstream from the ligand binding domain and membrane spanning region. Most FGF receptors contain a tyrosine kinase motif downstream from the ligand binding domain and membrane spanning region. Since FGF is implicated in a variety of growth disorders and cancers, it seems reasonable that blocking the FGF signal activity via inhibition of the tyrosine activity would be of therapeutic value. So, there is currently a search for good inhibitors of this system.

This crystal structure for 1FGI is from an engineered protein that represents residues 404-761 (sequence below) of the human FGF receptor 1 (FGFR 1). The X-ray structure of the unit cell dimer (Kinemage 1 and Kinemage 2 ) shows that the inhibitor SU-5402 {3-[(3-(2-carboxyethyl)-4-methylpyrrol-2-yl)methylene]-2-indolinone} resides in a cleft between the two distinct lobes of the tyrosine kinase domain of the receptor, with the oxy-indole ring near the volume occupied by the adenine base of ATP. (This is easiest to visualize in Kinemage 3). The characteristics of the unit cell for this structure are summarized at pdbsum.

The SU-5402 inhibitor resides in a cleft of the tyrosine binding region of FGFR 1 that is defined by hydrophobic residues Leu-484, Phe-489, Val-492, Ile-545, Val-561, Tyr-563, Ala-254, and Gly-567. The position of the SU-5402 inhibitor within the binding cleft is anchored by hydrogen bonding between the inhibitor oxyindole ring N1 and the backbone carbonyl of Glu-562, the backbone amide of Ala-564 to the oxyindole ring carbonyl, and the side chain amide of Asn-568 to oxygen of the inhibitor carboxyethyl group.

Of particular significance is the oxy-aromatic interactions of the hydrogen atoms of the plane of Phe-489. All five phenyl group hydrogens are interacting with near-by oxygen atoms: each of the two oxygen atoms of the inhibitor carboxyethyl group, the backbone carbonyl of Arg-627 and the side chain oxygen atoms of Asn-628 and Asp-641. This network of oxy-aromatic interactions and hydrogen bonds most likely explains the preference of SU-5402 for the FGFR 1 receptor. Also, the area of this receptor's "phenyl loop" is disordered with other inhibitors, but quite well resolved with SU-5402, These interactions are highlighted in Kinemage 4.

The SYBYL stick rendering of SU-5402 and the surface contour of this compound within the binding cleft of the Tyrosine Kinase Domain of FGFR 1 is shown below:

Atom	Color	Structure	Color
Carbon	white	Peptide alpha	magenta
Hydrogen	cyan	Peptide beta	yellow
Oxygen	red	Peptide coil	cyan
Nitrogen	blue	Inhibitor Surface	green dots

The real-time visualization using KiNG of the structures on this site requires a java-enabled (JRE from Java) browser.

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View 1 The Dimer
View 2 Binding Cleft, Chain A from "front"
View 3 Binding Cleft, Chain A from "top"
View 4 Binding Cleft, Chain B from "front"
View 5 Binding Cleft, Chain B from "top"

This kinemage adds main chain, side chains, main chain hydrogen bonds, ribbon and cartoon rendering to kinemage 1.

View 1 The Dimer
View 2 Binding Cleft, Chain A from "front"
View 3 Binding Cleft, Chain A from "top"
View 4 Binding Cleft, Chain B from "front"
View 5 Binding Cleft, Chain B from "top"

Kinemage 4: Inhibitor SU-5402 Bound To FGFR 1 Tyrosine Kinase Domain Interactions

The SU-5402 inhibitor resides in a cleft defined by hydrophobic residues Leu-484, Phe-489, Val-492, Ile-545, Val-561, Tyr-563, Ala-564, and Gly-567. The position of the SU-5402 inhibitor within the binding cleft is anchored by hydrogen bonding between the inhibitor oxyindole ring N1 and the backbone carbonyl of Glu-562, the backbone amide of Ala-564 to the oxyindole ring carbonyl, and the side chain amide of Asn-628 to oxygen of the inhibitor carboxyethyl group. All five phenyl group hydrogens are interacting with near-by oxygen atoms: each of the two oxygen atoms of the inhibitor carboxyethyl group, the backbone carbonyl of Arg-627 and the side chain oxygen atoms of Asn-628 and Asp-641.

View 1 The Monomer
View 2 Binding Cleft, "front"
View 3 Binding Cleft, "top"
View 4 H Bonding Interactions
View 5 Oxy-aromatic interactions

Sequence: The X-ray resolved residues span residues 464-762 of the human FGFR 1 sequence

Unresolved N-terminal: MVAGVSEY

X-ray resolved: ELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKM
LKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEY
SYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHI
DYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRM
DKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTS

Unresolved C-terminal: NQE

Residues 464-762 of human FGFR 1 was isolated from transfected Spodoptera frugiperda insect cells; structural coordinates were taken from the Brookhaven Database file 1FGI.

The engineered sequence contained three residues that were different from human:
Cys-488 and 584 were changed to Ser to prevent disulfide oligiomerization.
Leu-457 was changed to Val to create an aNcol cloning site.


Stick View of Su-5402	Inhibitor Surface Within Tyrosine Kinase Domain

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Click on KiNG to see	The Unit Cell

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Click on KiNG to see	Cartoon Rendering

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Click on KiNG to see	Monomer of the Inhibitor-Receptor Complex

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Click on KiNG to see	Inhibitor-Receptor Interactions