HEADER DNA 26-FEB-22 7X2Z TITLE NMR SOLUTION STRUCTURE OF THE 1:1 COMPLEX OF A PYRIDOSTATIN DERIVATIVE TITLE 2 (PYPDS) BOUND TO A G-QUADRUPLEX MYT1L COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-QUADRUPLEX DNA MYT1L; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR L.-Y.LIU,Z.-W.MAO,W.LIU REVDAT 3 14-JUN-23 7X2Z 1 REMARK REVDAT 2 21-DEC-22 7X2Z 1 JRNL REVDAT 1 08-JUN-22 7X2Z 0 JRNL AUTH L.-Y.LIU,T.Z.MA,Y.L.ZENG,W.LIU,Z.-W.MAO JRNL TITL STRUCTURAL BASIS OF PYRIDOSTATIN AND ITS DERIVATIVES JRNL TITL 2 SPECIFICALLY BINDING TO G-QUADRUPLEXES. JRNL REF J.AM.CHEM.SOC. V. 144 11878 2022 JRNL REFN ESSN 1520-5126 JRNL PMID 35749293 JRNL DOI 10.1021/JACS.2C04775 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7X2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300026302. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298 REMARK 210 PH : 7.0; 7.0; 7.0 REMARK 210 IONIC STRENGTH : 40; 40; 0 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1.20 MM / MYT1L, 1.20 MM / REMARK 210 PYPDS, 90% H2O/10% D2O; 10 MM / REMARK 210 PYPDS, DMSO; 1.20 MM / MYT1L, 90% REMARK 210 H2O/10% D2O; 1.20 MM / MYT1L, REMARK 210 1.20 MM / PYPDS, 100% D2O; 1.20 REMARK 210 MM / MYT1L, 0.60 MM / PYPDS, 90% REMARK 210 H2O/10% D2O; 0.1 MM [U-15N]-GUA REMARK 210 MYT1L_15N, 0.1 MM / PYPDS, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR VERSION 3.1, NMRFAM REMARK 210 -SPARKY 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DA A 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 5 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG A 6 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 6 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DA A 7 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DA A 7 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 DA A 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 10 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DA A 12 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DA A 12 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 13 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DG A 13 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 13 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DC A 14 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DT A 15 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 15 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC A 16 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DT A 17 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 18 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 18 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 18 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DG A 19 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DG A 19 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG A 19 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 DG A 20 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 20 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 20 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DT A 21 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT A 22 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1024 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36470 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF THE 1:1 COMPLEX OF A PYRIDOSTATIN REMARK 900 DERIVATIVE (PYPDS) BOUND TO A G-QUADRUPLEX MYT1L DBREF 7X2Z A 1 29 PDB 7X2Z 7X2Z 1 29 SEQRES 1 A 29 DA DG DG DG DA DG DA DG DG DA DG DA DG SEQRES 2 A 29 DC DT DC DT DG DG DG DT DT DG DG DG DT SEQRES 3 A 29 DG DG DG HET 7U0 A 101 99 HETNAM 7U0 4-(2-AZANYLETHOXY)-N2,N6-BIS[4-(2-PYRROLIDIN-1- HETNAM 2 7U0 YLETHOXY)QUINOLIN-2-YL]PYRIDINE-2,6-DICARBOXAMIDE FORMUL 2 7U0 C39 H44 N8 O5 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