HEADER DNA 01-MAR-01 1I5V TITLE SOLUTION STRUCTURE OF 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO- TITLE 2 ETHANOL INTERCALATED IN THE DNA DUPLEX D(CGATCG)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*AP*TP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DRUG-DNA COMPLEX, DOUBLE HELIX EXPDTA SOLUTION NMR NUMMDL 22 AUTHOR A.FAVIER,M.BLACKLEDGE,J.P.SIMORRE,D.MARION,J.C.DEBOUSY REVDAT 4 24-FEB-09 1I5V 1 VERSN REVDAT 3 01-APR-03 1I5V 1 JRNL REVDAT 2 22-AUG-01 1I5V 1 JRNL REVDAT 1 14-MAR-01 1I5V 0 JRNL AUTH A.FAVIER,M.BLACKLEDGE,J.P.SIMORRE,S.CROUZY, JRNL AUTH 2 V.DABOUIS,A.GUEIFFIER,D.MARION,J.C.DEBOUZY JRNL TITL SOLUTION STRUCTURE OF JRNL TITL 2 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL JRNL TITL 3 INTERCALATED IN THE DNA DUPLEX D(CGATCG)2. JRNL REF BIOCHEMISTRY V. 40 8717 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11467931 JRNL DOI 10.1021/BI0024963 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CALCULATION FROM RANDOMIZED REMARK 3 CARTESIAN COORDINATES REMARK 4 REMARK 4 1I5V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAR-01. REMARK 100 THE RCSB ID CODE IS RCSB012942. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 7 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM 2-(PYRIDO[1,2-E]PURIN-4- REMARK 210 YL)AMINO-ETHANOL, 2MM D(CGATCG)2 160 MM KCL, 0.15 MM EDTA, 20 REMARK 210 MM SODIUM PHOSPHATE; 2 MM 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO- REMARK 210 ETHANOL, 2MM D(CGATCG)2 160 MM KCL, 0.15 MM EDTA, 20 MM SODIUM REMARK 210 PHOSPHATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, TOCSY, 1H REMARK 210 -1H CT COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 600 MHZ, 400 MHZ REMARK 210 SPECTROMETER MODEL : INOVA, AMX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.A, FELIX, INSIGHT 97, REMARK 210 DISCOVER REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 22 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMER REMARK 210 MODELS ARE THE 22 STRUCTURES REMARK 210 WITH THE LOWEST EXPERIMENTAL REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 12 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG B 6 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC B 1 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT B 4 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 4 DG A 6 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 4 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DA B 3 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DT B 4 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 4 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 5 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 DC B 1 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 5 DG B 2 C1' - O4' - C4' ANGL. DEV. = -8.1 DEGREES REMARK 500 5 DG B 2 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DT B 4 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 5 DT B 4 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 6 DT A 4 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 6 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 6 DC B 1 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 6 DT B 4 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 DT B 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 7 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 7 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 7 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 DC B 1 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 7 DC B 1 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 DG B 2 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 7 DG B 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 7 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 8 DC A 1 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 136 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 1 DC A 1 0.07 SIDE_CHAIN REMARK 500 1 DC A 5 0.14 SIDE_CHAIN REMARK 500 1 DG A 6 0.15 SIDE_CHAIN REMARK 500 1 DG B 2 0.08 SIDE_CHAIN REMARK 500 1 DC B 5 0.14 SIDE_CHAIN REMARK 500 1 DG B 6 0.14 SIDE_CHAIN REMARK 500 2 DC A 1 0.06 SIDE_CHAIN REMARK 500 2 DA A 3 0.07 SIDE_CHAIN REMARK 500 2 DG A 6 0.13 SIDE_CHAIN REMARK 500 2 DC B 1 0.08 SIDE_CHAIN REMARK 500 2 DG B 2 0.07 SIDE_CHAIN REMARK 500 2 DC B 5 0.13 SIDE_CHAIN REMARK 500 2 DG B 6 0.16 SIDE_CHAIN REMARK 500 3 DC A 1 0.07 SIDE_CHAIN REMARK 500 3 DG A 2 0.09 SIDE_CHAIN REMARK 500 3 DC A 5 0.10 SIDE_CHAIN REMARK 500 3 DG A 6 0.16 SIDE_CHAIN REMARK 500 3 DG B 2 0.07 SIDE_CHAIN REMARK 500 3 DG B 6 0.14 SIDE_CHAIN REMARK 500 4 DG A 2 0.07 SIDE_CHAIN REMARK 500 4 DC A 5 0.07 SIDE_CHAIN REMARK 500 4 DG A 6 0.16 SIDE_CHAIN REMARK 500 4 DC B 1 0.06 SIDE_CHAIN REMARK 500 4 DC B 5 0.09 SIDE_CHAIN REMARK 500 4 DG B 6 0.16 SIDE_CHAIN REMARK 500 5 DC A 1 0.07 SIDE_CHAIN REMARK 500 5 DC A 5 0.07 SIDE_CHAIN REMARK 500 5 DG A 6 0.14 SIDE_CHAIN REMARK 500 5 DC B 1 0.09 SIDE_CHAIN REMARK 500 5 DC B 5 0.12 SIDE_CHAIN REMARK 500 5 DG B 6 0.13 SIDE_CHAIN REMARK 500 6 DC A 5 0.08 SIDE_CHAIN REMARK 500 6 DG A 6 0.17 SIDE_CHAIN REMARK 500 6 DC B 1 0.14 SIDE_CHAIN REMARK 500 6 DG B 2 0.06 SIDE_CHAIN REMARK 500 6 DA B 3 0.08 SIDE_CHAIN REMARK 500 6 DC B 5 0.11 SIDE_CHAIN REMARK 500 6 DG B 6 0.16 SIDE_CHAIN REMARK 500 7 DC A 1 0.09 SIDE_CHAIN REMARK 500 7 DC A 5 0.09 SIDE_CHAIN REMARK 500 7 DG A 6 0.16 SIDE_CHAIN REMARK 500 7 DC B 1 0.07 SIDE_CHAIN REMARK 500 7 DG B 2 0.06 SIDE_CHAIN REMARK 500 7 DA B 3 0.06 SIDE_CHAIN REMARK 500 7 DC B 5 0.07 SIDE_CHAIN REMARK 500 7 DG B 6 0.16 SIDE_CHAIN REMARK 500 8 DG A 2 0.08 SIDE_CHAIN REMARK 500 8 DC A 5 0.10 SIDE_CHAIN REMARK 500 8 DG A 6 0.13 SIDE_CHAIN REMARK 500 8 DG B 6 0.15 SIDE_CHAIN REMARK 500 9 DC A 5 0.10 SIDE_CHAIN REMARK 500 9 DG A 6 0.14 SIDE_CHAIN REMARK 500 9 DC B 5 0.06 SIDE_CHAIN REMARK 500 9 DG B 6 0.16 SIDE_CHAIN REMARK 500 10 DG A 2 0.08 SIDE_CHAIN REMARK 500 10 DG A 6 0.14 SIDE_CHAIN REMARK 500 10 DC B 1 0.11 SIDE_CHAIN REMARK 500 10 DG B 2 0.07 SIDE_CHAIN REMARK 500 10 DC B 5 0.08 SIDE_CHAIN REMARK 500 10 DG B 6 0.15 SIDE_CHAIN REMARK 500 11 DC A 5 0.15 SIDE_CHAIN REMARK 500 11 DG A 6 0.14 SIDE_CHAIN REMARK 500 11 DC B 1 0.08 SIDE_CHAIN REMARK 500 11 DC B 5 0.10 SIDE_CHAIN REMARK 500 11 DG B 6 0.14 SIDE_CHAIN REMARK 500 12 DC A 1 0.09 SIDE_CHAIN REMARK 500 12 DC A 5 0.09 SIDE_CHAIN REMARK 500 12 DG A 6 0.17 SIDE_CHAIN REMARK 500 12 DC B 5 0.07 SIDE_CHAIN REMARK 500 12 DG B 6 0.17 SIDE_CHAIN REMARK 500 13 DC A 1 0.06 SIDE_CHAIN REMARK 500 13 DC A 5 0.10 SIDE_CHAIN REMARK 500 13 DG A 6 0.17 SIDE_CHAIN REMARK 500 13 DC B 1 0.11 SIDE_CHAIN REMARK 500 13 DC B 5 0.11 SIDE_CHAIN REMARK 500 13 DG B 6 0.15 SIDE_CHAIN REMARK 500 14 DG A 2 0.08 SIDE_CHAIN REMARK 500 14 DA A 3 0.07 SIDE_CHAIN REMARK 500 14 DG A 6 0.13 SIDE_CHAIN REMARK 500 14 DG B 6 0.15 SIDE_CHAIN REMARK 500 15 DC A 1 0.08 SIDE_CHAIN REMARK 500 15 DC A 5 0.08 SIDE_CHAIN REMARK 500 15 DG A 6 0.13 SIDE_CHAIN REMARK 500 15 DC B 5 0.10 SIDE_CHAIN REMARK 500 15 DG B 6 0.16 SIDE_CHAIN REMARK 500 16 DG A 6 0.15 SIDE_CHAIN REMARK 500 16 DG B 2 0.07 SIDE_CHAIN REMARK 500 16 DG B 6 0.13 SIDE_CHAIN REMARK 500 17 DG A 2 0.06 SIDE_CHAIN REMARK 500 17 DC A 5 0.10 SIDE_CHAIN REMARK 500 17 DG A 6 0.15 SIDE_CHAIN REMARK 500 17 DC B 5 0.07 SIDE_CHAIN REMARK 500 17 DG B 6 0.13 SIDE_CHAIN REMARK 500 18 DC A 5 0.11 SIDE_CHAIN REMARK 500 18 DG A 6 0.16 SIDE_CHAIN REMARK 500 18 DC B 1 0.14 SIDE_CHAIN REMARK 500 18 DG B 6 0.20 SIDE_CHAIN REMARK 500 19 DG A 6 0.14 SIDE_CHAIN REMARK 500 19 DC B 1 0.07 SIDE_CHAIN REMARK 500 19 DG B 2 0.07 SIDE_CHAIN REMARK 500 19 DC B 5 0.11 SIDE_CHAIN REMARK 500 19 DG B 6 0.17 SIDE_CHAIN REMARK 500 20 DC A 1 0.07 SIDE_CHAIN REMARK 500 20 DC A 5 0.12 SIDE_CHAIN REMARK 500 20 DG A 6 0.14 SIDE_CHAIN REMARK 500 20 DC B 1 0.07 SIDE_CHAIN REMARK 500 20 DC B 5 0.06 SIDE_CHAIN REMARK 500 20 DG B 6 0.16 SIDE_CHAIN REMARK 500 21 DC A 1 0.06 SIDE_CHAIN REMARK 500 21 DG A 2 0.07 SIDE_CHAIN REMARK 500 21 DC A 5 0.09 SIDE_CHAIN REMARK 500 21 DG A 6 0.15 SIDE_CHAIN REMARK 500 21 DG B 6 0.15 SIDE_CHAIN REMARK 500 22 DC A 5 0.07 SIDE_CHAIN REMARK 500 22 DG A 6 0.15 SIDE_CHAIN REMARK 500 22 DG B 2 0.09 SIDE_CHAIN REMARK 500 22 DG B 6 0.15 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 PPZ A 7 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPZ B 7 DBREF 1I5V A 1 6 PDB 1I5V 1I5V 1 6 DBREF 1I5V B 1 6 PDB 1I5V 1I5V 1 6 SEQRES 1 A 6 DC DG DA DT DC DG SEQRES 1 B 6 DC DG DA DT DC DG HET PPZ A 7 28 HET PPZ B 7 28 HETNAM PPZ 2-(PYRIDO[1,2-E]PURIN-4-YL)AMINO-ETHANOL FORMUL 3 PPZ 2(C11 H11 N5 O) SITE 1 AC1 4 DC A 5 DG A 6 DC B 1 DG B 2 SITE 1 AC2 4 DC A 1 DG A 2 DC B 5 DG B 6 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 266 0 2 0 0 0 2 6 0 0 0 2 END