Supplementary Figure S1. Supplementary Figure S1. Chemical structure of CH

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1 Supplementary Figure S1 Supplementary Figure S1. Chemical structure of CH

2 Supplementary Figure S2 Kinase % competition TRKA 99 TRKC 95 TRKB 92 MEK5 87 AXL 84 CLK1 82 MERTK 82 GCN2 (Kin.Dom.2,S808G) 73 LOK 71 Supplementary Figure S2. Kinase selectivity profile of 100 nm CH against 468 kinases in the KINOMEscan scanmax panel.

3 Supplementary Figure S3 Conc. (ng/ml) CH , 0.1mg/kg, PO CH , 0.3mg/kg, PO 10 CH , 1mg/kg, PO 1 CH , 3mg/kg, PO CH , 10mg/kg, PO Time (h) Dose AUC last t 1/2 T max C max mg/kg ng*h/ml h h ng/ml Supplementary Figure S3. Plasma concentration-time curves and pharmacokinetic parameters of repeated daily oral administration (11 days) of CH in a mouse xenograft study

4 Supplementary Figure S4 Ki-67 positive cells (/1,000 cells) TUNEL-positive cells (/1,000 cells) A Control CH mg/kg CH mg/kg Ki-67 TUNEL B 600 Ki-67 TUNEL Control 3 mg/kg 10 mg/kg 0 Supplementary Figure S4. Inhibition of proliferation and induction of apoptosis by CH Mice bearing subcutaneous CUTO-3 tumors were dosed orally with 3 or 10 mg/kg of CH once a day for 3 days (n = 3). Six hours after the last administration, tumors were resected, fixed, and embedded in paraffin. Sections were stained with a Ki-67 antibody and by the TUNEL method (A). Numbers of stained cells per 1,000 cells were counted (B).

5 Supplementary Figure S5 AGA (Arg) ATA (Ile) 5 3 Supplementary Figure S5. Electropherogram of Sanger sequencing showing the R280I mutation in the TP53 gene in CUTO-3. The sequencing was performed as described previously (Ref. 26)

6 Supplementary Table S2 Data collection X-ray source CMCF-08ID (CLS 1 ) Wavelength [Å] Detector Rayonix 300 Temperature [K] 100 Space group H 3 2 Cell: a; b; c [Å] ; ; α; β; γ [ ] 90.0; 90.0; Resolution [Å] 2.76 ( ) 2 Unique reflections (2525) 2 Multiplicity 4.9 (5.0) 2 Completeness [%] 99.7 (100.0) 2 R sym [%] 11.9 (43.5) 2 R meas [%] 13.2 (48.1) 2 Mean(I)/sd (4.64) 2 Refinement 4 Resolution [Å] Number of reflections (working / test) / 721 R cryst [%] 20.6 R free [%] Total number of atoms: Protein 2426 Water 28 Ligand 41 Deviation from ideal geometry: 6 Bond lengths [Å] Bond angles [ ] 1.20 Bonded B s [Å] Ramachandran plot: 8 Most favored regions [%] 92.3 Additional allowed regions [%] 7.7 Generously allowed regions [%] 0.0 Disallowed regions [%] CANADIAN LIGHT SOURCE (CLS, Saskatoon, Canada) 2 Values in parenthesis refer to the highest resolution bin. 3 Calculated from independent reflections 4 Values as defined in REFMAC5, without sigma cut-off 5 Test-set contains 6.4% of measured reflections 6 Root mean square deviations from geometric target values 7 Calculated with MOLEMAN 8 Calculated with PROCHECK Supplementary Table S2. Crystallographic data collection and refinement statistics for TRKA in complex with CH

7 Supplementary Table S3 Time 4 h 24 h Gene name Average fold change PHLDA SPRED ETV FOSL CCND EPHA SPRY DUSP BMF 5.9 SULT1A3 5.7 KLHL WDR PAQR AURKB 0.30 PSMC3IP 0.29 IGFBP ASF1B 0.27 RAD POLA CDC42EP CDCA CENPM 0.25 FEN MCM EXO E2F TRIP Time 24 h Gene name Average fold change UHRF DSCC GLB1L ETV TNC 0.22 DTL 0.22 MCM MCM TUBA1B 0.21 MYBL MCM MCM TESC 0.20 TUBA4A 0.20 TYMS 0.20 CCND RRM GINS CDC CDC MFSD2A 0.12 SPRY ETV FOSL ETV DUSP Supplementary Table S3. Genes commonly upregulated or downregulated in CUTO-3 and KM12- Luc cells by 4- or 24-hour CH treatment.

8 Supplementary Table S4 Time Upstream Regulator Predicted Activation State Activation z-score p-value of overlap 4 h Mek Inhibited E h E2f Inhibited E-20 ERBB2 Inhibited E-17 Mek Inhibited E-10 MITF Inhibited E-07 AREG Inhibited E-07 RABL6 Inhibited E-07 Cg Inhibited E-06 E2F6 Activated E-18 TP53 Activated E-06 NUPR1 Activated E-04 Supplementary Table S4. Upstream regulators inhibited or activated by CH were identified with IPA by analyzing the commonly changed genes in 4- or 24-hour CH treatment in CUTO-3 and KM12-Luc.

9 Supplementary Table S5 A to B Papp (cm/s) B to A Efflux ratio 1.46E E Papp: Apparent permeability; A, apical; B, basolateral Supplementary Table S5. Bidirectional flux of 1 μm CH in Caco-2 cells. The Caco-2 permeability assay was performed as described previously (Ref. 30)