2K4L - Header Asymmetric Unit

HEADER DNA 13-JUN-08 2K4L

TITLE SOLUTION STRUCTURE OF A 2:1C2-(2-NAPHTHYL)PYRROLO[2,1-C][1, TITLE 2 4]BENZODIAZEPINE (PBD) DNA ADDUCT: MOLECULAR BASIS FOR UNEXPECTEDLY TITLE 3 HIGH DNA HELIX STABILIZATION.

COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*D COMPND 3 T)-3'; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE 14-MER NUCLEOTIDE SEQUENCE AATCTTTAAAGATT WAS SOURCE 4 SYNTHESISED USING AN APPLIED BIOSYSTEMS DNA SYNTHESIZER. THE DNA SOURCE 5 SEQUENCE WAS PURIFIED BY REVERSED-PHASE HPLC AT ROOM TEMPERATURE. SOURCE 6 THE DUPLEX WAS FORMED BY ANNEALING IN PHOSPHATE BUFFER.

KEYWDS PYRROLO[2, 1-C][1, 4]BENZODIAZEPINE, PBD, DNA ADDUCT, DNA

EXPDTA SOLUTION NMR

NUMMDL 10

AUTHOR D.ANTONOW,T.BARATA,T.C.JENKINS,G.N.PARKINSON,P.W.HOWARD,D.E.THURSTON, AUTHOR 2 M.ZLOH

REVDAT 3 11-AUG-10 2K4L 1 JRNL REVDAT 2 24-FEB-09 2K4L 1 VERSN REVDAT 1 28-OCT-08 2K4L 0

JRNL AUTH D.ANTONOW,T.BARATA,T.C.JENKINS,G.N.PARKINSON,P.W.HOWARD, JRNL AUTH 2 D.E.THURSTON,M.ZLOH JRNL TITL SOLUTION STRUCTURE OF A 2:1 C2-(2-NAPHTHYL) JRNL TITL 2 PYRROLO[2,1-C][1,4]BENZODIAZEPINE DNA ADDUCT: MOLECULAR JRNL TITL 3 BASIS FOR UNEXPECTEDLY HIGH DNA HELIX STABILIZATION. JRNL REF BIOCHEMISTRY V. 47 11818 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18925745 JRNL DOI 10.1021/BI801225Q

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.ANTONOW,N.COOPER,P.W.HOWARD,D.E.THURSTON REMARK 1 TITL PARALLEL SYNTHESIS OF A NOVEL C2-ARYL REMARK 1 TITL 2 PYRROLO[2,1-C][1,4]BENZODIAZEPINE (PBD) LIBRARY REMARK 1 REF J.COMB.CHEM. V. 9 437 2007 REMARK 1 REFN ISSN 1520-4766 REMARK 1 PMID 17397227 REMARK 1 DOI 10.1021/CC0601332

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.16 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCES RESTRAINTS WERE CALCULATED REMARK 3 FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REMARK 3 REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL REMARK 3 DISTANCE CONSTRAINTS WERE CLASSIFIED ACCORDING TO CROSSPEAK REMARK 3 INTENSITIES AS (S) STRONG (1.80 TO 2.90), (M) MEDIUM (1.80 TO REMARK 3 4.00) AND (W) WEAK (D = 4.0, -2.2/+1.0 ). DISTANCE CONSTRAINS REMARK 3 WITH METHYL PROTONS WERE CONSIDERED SEPARATELY (D = 4.0 , -2.2/+ REMARK 3 1.5 ). THE SIMULATED ANNEALING APPROACH WAS USED TO GENERATE 200 REMARK 3 STRUCTURES. THE 10 LOWEST ENERGY STRUCTURES WERE CHOSEN AND THE REMARK 3 ROOT MEAN SQUARE DEVIATION VALUES CALCULATED.

REMARK 4 REMARK 4 2K4L COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB100668.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.85 REMARK 210 IONIC STRENGTH : 130 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.68 MM DNA (5'-D(*(DA)P*(DA)P* REMARK 210 (DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT) REMARK 210 P*(DT))-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 1.3, AMIX 3.5.5 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT B 25 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT B 26 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT B 33 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT B 34 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DT B 25 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DT B 26 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT B 33 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 3 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 DT B 25 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 DT B 26 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DT B 33 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 4 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 4 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 4 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT B 25 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 4 DT B 26 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 4 DT B 33 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 5 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 5 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 5 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 DT B 25 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 5 DT B 26 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DT B 33 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 6 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 6 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 6 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 6 DT A 14 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 6 DT B 25 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 6 DT B 34 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 7 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 7 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 7 DA A 9 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 7 DT A 13 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 7 DT B 25 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 7 DA B 29 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 7 DT B 33 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 8 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 8 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 8 DA A 9 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 8 DT A 13 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 68 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 DG B 31 0.05 SIDE CHAIN REMARK 500 8 DG B 31 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PZD A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PZD B 102

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15613 RELATED DB: BMRB

DBREF 2K4L A 1 14 PDB 2K4L 2K4L 1 14 DBREF 2K4L B 21 34 PDB 2K4L 2K4L 21 34

SEQRES 1 A 14 DA DA DT DC DT DT DT DA DA DA DG DA DT SEQRES 2 A 14 DT SEQRES 1 B 14 DA DA DT DC DT DT DT DA DA DA DG DA DT SEQRES 2 B 14 DT

HET PZD A 101 50 HET PZD B 102 50

HETNAM PZD (11AS)-7,8-DIMETHOXY-2-NAPHTHALEN-2-YL-1,10,11,11A- HETNAM 2 PZD TETRAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE

FORMUL 3 PZD 2(C24 H22 N2 O3)

LINK N2 DG A 11 C9A PZD A 101 1555 1555 1.46 LINK N2 DG B 31 C9A PZD B 102 1555 1555 1.46

SITE 1 AC1 8 DG A 11 DA A 12 DT A 13 DT A 14 SITE 2 AC1 8 DC B 24 DT B 25 DT B 26 DT B 27 SITE 1 AC2 9 DT A 3 DC A 4 DT A 5 DT A 6 SITE 2 AC2 9 DT A 7 DG B 31 DA B 32 DT B 33 SITE 3 AC2 9 DT B 34

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