HEADER DNA 08-FEB-10 2KTT TITLE SOLUTION STRUCTURE OF A COVALENTLY BOUND PYRROLO[2,1-C][1, TITLE 2 4]BENZODIAZEPINE-BENZIMIDAZOLE HYBRID TO A 10MER DNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA DUPLEX, PYRROLOBENZODIAZEPINE, PBD-BENZIMIDAZOLE HYBRID, DNA-DRUG KEYWDS 2 COMPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR M.RETTIG,M.WEINGARTH,W.LANGEL,A.KAMAL,P.P.KUMAR,K.WEISZ REVDAT 2 01-MAY-24 2KTT 1 REMARK DBREF LINK REVDAT 1 09-MAR-10 2KTT 0 JRNL AUTH M.RETTIG,M.WEINGARTH,W.LANGEL,A.KAMAL,P.P.KUMAR,K.WEISZ JRNL TITL SOLUTION STRUCTURE OF A COVALENTLY BOUND JRNL TITL 2 PYRROLO[2,1-C][1,4]BENZODIAZEPINE-BENZIMIDAZOLE HYBRID TO A JRNL TITL 3 10MER DNA DUPLEX. JRNL REF BIOCHEMISTRY V. 48 12223 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19911838 JRNL DOI 10.1021/BI901655T REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KTT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000101564. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295; 283 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 0.28; 0.28 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DNA (5' REMARK 210 -D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3')-1, 1 MM PYRROLO[2,1-C][1,4] REMARK 210 BENZODIAZEPINE-BENZIMIDAZOLE HYBRID-2, 100 MM NACL-3, 20 MM PO4- REMARK 210 4, 100% D2O; 1 MM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3')-5, REMARK 210 1 MM PYRROLO[2,1-C][1,4]BENZODIAZEPINE-BENZIMIDAZOLE HYBRID-6, REMARK 210 100 MM NACL-7, 20 MM PO4-8, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D DQF-COSY; 2D REMARK 210 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : REPRESENTATIVE CONFORMERS OF REMARK 210 CLUSTERS 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HO5' DA B 11 OP1 DA B 12 1.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 DA A 1 C8 DA A 1 N9 0.078 REMARK 500 2 DA A 2 N3 DA A 2 C4 0.093 REMARK 500 2 DA A 2 C6 DA A 2 N6 -0.066 REMARK 500 2 DC A 3 P DC A 3 O5' -0.069 REMARK 500 2 DC A 3 N3 DC A 3 C4 -0.064 REMARK 500 2 DA A 4 C6 DA A 4 N1 -0.043 REMARK 500 2 DA A 4 N9 DA A 4 C4 0.046 REMARK 500 2 DA A 4 C6 DA A 4 N6 -0.060 REMARK 500 2 DA A 5 C6 DA A 5 N1 -0.078 REMARK 500 2 DA A 5 C8 DA A 5 N9 -0.054 REMARK 500 2 DT A 6 C3' DT A 6 C2' 0.094 REMARK 500 2 DT A 6 C5 DT A 6 C6 0.051 REMARK 500 2 DT A 7 P DT A 7 O5' 0.101 REMARK 500 2 DT A 7 C4' DT A 7 C3' 0.081 REMARK 500 2 DT A 7 N1 DT A 7 C2 0.056 REMARK 500 2 DT A 7 C5 DT A 7 C6 0.055 REMARK 500 2 DT A 7 O3' DG A 8 P -0.074 REMARK 500 2 DG A 8 N3 DG A 8 C4 0.048 REMARK 500 2 DT A 9 N1 DT A 9 C2 0.066 REMARK 500 2 DT A 10 C5' DT A 10 C4' 0.053 REMARK 500 2 DT A 10 N1 DT A 10 C2 -0.055 REMARK 500 2 DT A 10 C2 DT A 10 N3 -0.082 REMARK 500 2 DT A 10 C5 DT A 10 C7 0.044 REMARK 500 2 DA B 11 C5 DA B 11 C6 0.066 REMARK 500 2 DA B 12 C5' DA B 12 C4' 0.043 REMARK 500 2 DA B 12 C4' DA B 12 C3' 0.082 REMARK 500 2 DA B 12 C5 DA B 12 C6 0.067 REMARK 500 2 DA B 12 C5 DA B 12 N7 0.049 REMARK 500 2 DC B 13 C2 DC B 13 N3 -0.064 REMARK 500 2 DC B 13 N3 DC B 13 C4 -0.043 REMARK 500 2 DA B 14 C4' DA B 14 C3' 0.075 REMARK 500 2 DA B 15 P DA B 15 O5' -0.075 REMARK 500 2 DA B 15 C2' DA B 15 C1' 0.069 REMARK 500 2 DA B 15 N3 DA B 15 C4 0.069 REMARK 500 2 DT B 16 O4' DT B 16 C4' -0.078 REMARK 500 2 DT B 16 C5 DT B 16 C6 0.049 REMARK 500 2 DT B 16 C5 DT B 16 C7 -0.052 REMARK 500 2 DT B 17 C5' DT B 17 C4' 0.057 REMARK 500 2 DT B 17 N1 DT B 17 C2 0.050 REMARK 500 2 DT B 17 C5 DT B 17 C6 0.044 REMARK 500 2 DT B 17 C2 DT B 17 O2 0.053 REMARK 500 2 DG B 18 C6 DG B 18 N1 -0.042 REMARK 500 2 DT B 19 N1 DT B 19 C2 0.063 REMARK 500 2 DT B 20 C2' DT B 20 C1' 0.065 REMARK 500 3 DA A 2 O4' DA A 2 C4' -0.077 REMARK 500 3 DA A 2 N3 DA A 2 C4 0.052 REMARK 500 3 DA A 2 N9 DA A 2 C4 -0.036 REMARK 500 3 DC A 3 C5' DC A 3 C4' 0.107 REMARK 500 3 DC A 3 C4 DC A 3 N4 -0.089 REMARK 500 3 DA A 4 O3' DA A 4 C3' -0.039 REMARK 500 REMARK 500 THIS ENTRY HAS 133 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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. = 3.7 DEGREES REMARK 500 1 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA A 1 N1 - C6 - N6 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DA A 2 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DA A 2 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DC A 3 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DC A 3 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 4 N1 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA A 5 N1 - C6 - N6 ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DT A 10 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA B 11 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DA B 11 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DA B 11 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA B 11 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DA B 12 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DA B 12 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 12 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DA B 12 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DA B 14 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA B 14 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 DA B 14 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DA B 14 N1 - C6 - N6 ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DA B 15 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DA B 15 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA B 15 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DA B 15 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DA A 1 O4' - C1' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DA A 1 O4' - C1' - N9 ANGL. DEV. = 11.8 DEGREES REMARK 500 2 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DA A 1 N1 - C6 - N6 ANGL. DEV. = -8.3 DEGREES REMARK 500 2 DA A 2 N1 - C2 - N3 ANGL. DEV. = -6.1 DEGREES REMARK 500 2 DA A 2 C2 - N3 - C4 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DA A 2 N3 - C4 - C5 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DA A 2 C5 - C6 - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DA A 2 C4 - C5 - N7 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DA A 2 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DA A 2 C6 - C5 - N7 ANGL. DEV. = 6.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 346 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 DA A 2 0.06 SIDE CHAIN REMARK 500 1 DA A 5 0.05 SIDE CHAIN REMARK 500 1 DT A 6 0.10 SIDE CHAIN REMARK 500 1 DA B 15 0.07 SIDE CHAIN REMARK 500 2 DA A 1 0.08 SIDE CHAIN REMARK 500 2 DA A 4 0.07 SIDE CHAIN REMARK 500 2 DT A 6 0.10 SIDE CHAIN REMARK 500 2 DG A 8 0.07 SIDE CHAIN REMARK 500 2 DA B 11 0.12 SIDE CHAIN REMARK 500 2 DA B 12 0.12 SIDE CHAIN REMARK 500 2 DA B 14 0.10 SIDE CHAIN REMARK 500 2 DA B 15 0.07 SIDE CHAIN REMARK 500 2 DT B 16 0.09 SIDE CHAIN REMARK 500 3 DA A 1 0.07 SIDE CHAIN REMARK 500 3 DT A 6 0.08 SIDE CHAIN REMARK 500 3 DG A 8 0.08 SIDE CHAIN REMARK 500 3 DT A 9 0.09 SIDE CHAIN REMARK 500 3 DT A 10 0.08 SIDE CHAIN REMARK 500 3 DA B 11 0.07 SIDE CHAIN REMARK 500 3 DA B 15 0.10 SIDE CHAIN REMARK 500 3 DT B 16 0.12 SIDE CHAIN REMARK 500 3 DT B 17 0.09 SIDE CHAIN REMARK 500 3 DG B 18 0.08 SIDE CHAIN REMARK 500 3 DT B 19 0.08 SIDE CHAIN REMARK 500 4 DA A 4 0.06 SIDE CHAIN REMARK 500 4 DT A 7 0.08 SIDE CHAIN REMARK 500 4 DT A 10 0.10 SIDE CHAIN REMARK 500 4 DA B 14 0.09 SIDE CHAIN REMARK 500 4 DT B 17 0.13 SIDE CHAIN REMARK 500 4 DT B 20 0.10 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 PBH A 22 DBREF 2KTT A 1 10 PDB 2KTT 2KTT 1 10 DBREF 2KTT B 11 20 PDB 2KTT 2KTT 11 20 SEQRES 1 A 10 DA DA DC DA DA DT DT DG DT DT SEQRES 1 B 10 DA DA DC DA DA DT DT DG DT DT HET PBH A 22 83 HETNAM PBH (11AS)-7-METHOXY-8-(3-{4-[6-(4-METHYLPIPERAZIN-1-YL)- HETNAM 2 PBH 1H-BENZIMIDAZOL-2-YL]PHENOXY}PROPOXY)-1,2,3,10,11,11A- HETNAM 3 PBH HEXAHYDRO-5H-PYRROLO[2,1-C][1,4]BENZODIAZEPIN-5-ONE FORMUL 3 PBH C34 H40 N6 O4 LINK N2 DG A 8 C11 PBH A 22 1555 1555 1.47 SITE 1 AC1 12 DA A 4 DT A 6 DT A 7 DG A 8 SITE 2 AC1 12 DT A 9 DC B 13 DA B 14 DA B 15 SITE 3 AC1 12 DT B 16 DT B 17 DG B 18 DT B 19 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