HEADER DNA/INHIBITOR 19-JUN-17 5W77 TITLE SOLUTION STRUCTURE OF THE MYC G-QUADRUPLEX BOUND TO SMALL MOLECULE DC- TITLE 2 34 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)- COMPND 4 3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS C-MYC PROMOTER DNA-INHIBITOR COMPLEX, C-MYC PROMOTER G-QUADRUPLEX, KEYWDS 2 DNA, DNA-INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR X.CHEN,K.J.WALTERS REVDAT 4 14-JUN-23 5W77 1 REMARK REVDAT 3 16-MAR-22 5W77 1 REMARK REVDAT 2 03-MAR-21 5W77 1 TITLE REMARK LINK REVDAT 1 24-OCT-18 5W77 0 JRNL AUTH D.R.CALABRESE,X.CHEN,E.C.LEON,S.M.GAIKWAD,Z.PHYO,W.M.HEWITT, JRNL AUTH 2 S.ALDEN,T.A.HILIMIRE,F.HE,A.M.MICHALOWSKI,J.K.SIMMONS, JRNL AUTH 3 L.B.SAUNDERS,S.ZHANG,D.CONNORS,K.J.WALTERS,B.A.MOCK, JRNL AUTH 4 J.S.SCHNEEKLOTH JR. JRNL TITL CHEMICAL AND STRUCTURAL STUDIES PROVIDE A MECHANISTIC BASIS JRNL TITL 2 FOR RECOGNITION OF THE MYC G-QUADRUPLEX. JRNL REF NAT COMMUN V. 9 4229 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30315240 JRNL DOI 10.1038/S41467-018-06315-W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.45 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5W77 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228513. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.2 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.3 MM DNA (5' REMARK 210 -D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP* REMARK 210 AP*A)-3'), 25 MM D11- TRIS, 50 MM POTASSIUM CHLORIDE, 90% H2O/10% REMARK 210 D2O; 0.125 MM DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP* REMARK 210 GP*GP*TP*GP*GP*GP*TP*AP*A)-3'), 0.25 MM (2R)-4-[4-(3- REMARK 210 METHYLPHENYL)-1H-1,2,3-TRIAZOL-1-YL]-1-(2,4,5-TRIFLUOROPHENYL) REMARK 210 BUTAN-2-AMINE, 25 MM D11- TRIS, 50 MM POTASSIUM CHLORIDE, 90% REMARK 210 H2O/10% D6-DMSO; 0.25 MM DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP* REMARK 210 GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3'), 0.50 MM (2R)-4-[4-(3- REMARK 210 METHYLPHENYL)-1H-1,2,3-TRIAZOL-1-YL]-1-(2,4,5-TRIFLUOROPHENYL) REMARK 210 BUTAN-2-AMINE, 25 MM D11- TRIS, 50 MM POTASSIUM CHLORIDE, 90% REMARK 210 D2O/10% D6-DMSO; 0.25 MM DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP* REMARK 210 GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*A)-3'), 0.5 MM SELECTIVE 13C- REMARK 210 LABELING (2R)-4-[4-(3-METHYLPHENYL)-1H-1,2,3-TRIAZOL-1-YL]-1-(2, REMARK 210 4,5-TRIFLUOROPHENYL)BUTAN-2-AMINE, 25 MM TRIS, 50 MM POTASSIUM REMARK 210 CHLORIDE, 90% D2O/10% D6-DMSO; 0.5 MM (2R)-4-[4-(3-METHYLPHENYL)- REMARK 210 1H-1,2,3-TRIAZOL-1-YL]-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-AMINE, REMARK 210 25 MM D11- TRIS, 50 MM POTASSIUM CHLORIDE, 90% D2O/10% D6-DMSO; REMARK 210 0.1 MM DNA (5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP* REMARK 210 TP*GP*GP*GP*TP*AP*A)-3'), 0.05-0.6 MM (2R)-4-[4-(3-METHYLPHENYL)- REMARK 210 1H-1,2,3-TRIAZOL-1-YL]-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-AMINE, REMARK 210 25 MM D11- TRIS, 50 MM POTASSIUM CHLORIDE, 90% H2O/10% D6-DMSO REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 3D 13C HALF- REMARK 210 FILTERED NOESY; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C HMBC; 1D 1H REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ; 800 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.5PL5, NMRPIPE 8.9, REMARK 210 XEASY, TALOS TALOS+ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 7 O6 REMARK 620 2 DG A 8 O6 73.3 REMARK 620 3 DG A 11 O6 76.7 91.1 REMARK 620 4 DG A 12 O6 133.9 74.0 72.3 REMARK 620 5 DG A 16 O6 116.4 155.9 71.3 84.7 REMARK 620 6 DG A 17 O6 152.3 107.9 130.2 69.8 74.1 REMARK 620 7 DG A 20 O6 72.5 128.0 117.3 152.9 75.8 86.7 REMARK 620 8 DG A 21 O6 91.5 72.0 161.8 108.2 126.9 63.9 70.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 8 O6 REMARK 620 2 DG A 9 O6 72.9 REMARK 620 3 DG A 12 O6 73.0 99.8 REMARK 620 4 DG A 13 O6 130.9 76.8 75.3 REMARK 620 5 DG A 17 O6 104.2 166.5 66.9 96.4 REMARK 620 6 DG A 18 O6 160.1 112.2 122.9 68.3 75.1 REMARK 620 7 DG A 21 O6 70.9 127.6 104.3 154.3 61.3 92.1 REMARK 620 8 DG A 22 O6 84.5 68.5 157.1 118.6 124.8 80.0 71.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9WP A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9WP A 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27144 RELATED DB: BMRB DBREF 5W77 A 4 25 PDB 5W77 5W77 4 25 SEQRES 1 A 22 DT DG DA DG DG DG DT DG DG DG DT DA DG SEQRES 2 A 22 DG DG DT DG DG DG DT DA DA HET K A 101 1 HET K A 102 1 HET 9WP A 103 57 HET 9WP A 104 57 HETNAM K POTASSIUM ION HETNAM 9WP 4-[(AZEPAN-1-YL)METHYL]-5-HYDROXY-2-METHYL-N-[4- HETNAM 2 9WP (TRIFLUOROMETHYL)PHENYL]-1-BENZOFURAN-3-CARBOXAMIDE FORMUL 2 K 2(K 1+) FORMUL 4 9WP 2(C24 H25 F3 N2 O3) LINK O6 DG A 7 K K A 101 1555 1555 2.82 LINK O6 DG A 8 K K A 101 1555 1555 2.92 LINK O6 DG A 8 K K A 102 1555 1555 2.92 LINK O6 DG A 9 K K A 102 1555 1555 3.04 LINK O6 DG A 11 K K A 101 1555 1555 2.95 LINK O6 DG A 12 K K A 101 1555 1555 2.90 LINK O6 DG A 12 K K A 102 1555 1555 2.97 LINK O6 DG A 13 K K A 102 1555 1555 3.07 LINK O6 DG A 16 K K A 101 1555 1555 2.94 LINK O6 DG A 17 K K A 101 1555 1555 2.90 LINK O6 DG A 17 K K A 102 1555 1555 3.04 LINK O6 DG A 18 K K A 102 1555 1555 2.85 LINK O6 DG A 20 K K A 101 1555 1555 2.90 LINK O6 DG A 21 K K A 101 1555 1555 2.96 LINK O6 DG A 21 K K A 102 1555 1555 3.04 LINK O6 DG A 22 K K A 102 1555 1555 3.03 SITE 1 AC1 9 DG A 7 DG A 8 DG A 11 DG A 12 SITE 2 AC1 9 DG A 16 DG A 17 DG A 20 DG A 21 SITE 3 AC1 9 K A 102 SITE 1 AC2 9 DG A 8 DG A 9 DG A 12 DG A 13 SITE 2 AC2 9 DG A 17 DG A 18 DG A 21 DG A 22 SITE 3 AC2 9 K A 101 SITE 1 AC3 5 DA A 6 DG A 7 DG A 11 DG A 16 SITE 2 AC3 5 DG A 20 SITE 1 AC4 5 DG A 9 DG A 13 DG A 18 DT A 23 SITE 2 AC4 5 DA A 25 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1