HEADER DNA/INHIBITOR 23-DEC-10 2L7V TITLE QUINDOLINE/G-QUADRUPLEX COMPLEX 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 KEYWDS C-MYC PROMOTER, DNA-INHIBITOR COMPLEX, C-MYC PROMOTER G-QUADRUPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.DAI,M.CARVER,R.MATHAD,D.YANG REVDAT 3 01-MAY-24 2L7V 1 REMARK LINK REVDAT 2 16-NOV-11 2L7V 1 JRNL REVDAT 1 09-NOV-11 2L7V 0 JRNL AUTH J.DAI,M.CARVER,L.H.HURLEY,D.YANG JRNL TITL SOLUTION STRUCTURE OF A 2:1 QUINDOLINE-C-MYC G-QUADRUPLEX: JRNL TITL 2 INSIGHTS INTO G-QUADRUPLEX-INTERACTIVE SMALL MOLECULE DRUG JRNL TITL 3 DESIGN. JRNL REF J.AM.CHEM.SOC. V. 133 17673 2011 JRNL REFN ISSN 0002-7863 JRNL PMID 21967482 JRNL DOI 10.1021/JA205646Q REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : INSIGHT II 2003 REMARK 3 AUTHORS : ACCELRYS SOFTWARE INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000102066. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 35 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 0.01 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 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'), 2 MM QUINDOLINE, 10 MM POTASSIUM PHOSPHATE, 0.1 MM REMARK 210 DSS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX 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 : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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 1 DA A 15 C5' DA A 15 C4' 0.058 REMARK 500 2 DA A 15 C5' DA A 15 C4' 0.051 REMARK 500 3 DA A 15 C5' DA A 15 C4' 0.051 REMARK 500 4 DA A 15 C5' DA A 15 C4' 0.055 REMARK 500 4 DG A 18 C5' DG A 18 C4' 0.042 REMARK 500 6 DA A 15 C5' DA A 15 C4' 0.056 REMARK 500 7 DA A 15 C5' DA A 15 C4' 0.048 REMARK 500 8 DA A 15 C5' DA A 15 C4' 0.046 REMARK 500 9 DA A 15 C5' DA A 15 C4' 0.054 REMARK 500 9 DG A 18 C5' DG A 18 C4' 0.043 REMARK 500 10 DA A 15 C5' DA A 15 C4' 0.056 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 DG A 9 C3' - O3' - P ANGL. DEV. = 7.9 DEGREES REMARK 500 1 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DA A 15 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 2 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DA A 15 C3' - O3' - P ANGL. DEV. = 11.1 DEGREES REMARK 500 2 DG A 21 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 3 DG A 12 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DA A 15 C3' - O3' - P ANGL. DEV. = 10.9 DEGREES REMARK 500 4 DG A 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 DG A 7 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DA A 15 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DA A 15 C3' - O3' - P ANGL. DEV. = 10.4 DEGREES REMARK 500 5 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 5 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 DA A 15 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES REMARK 500 6 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 6 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 6 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 6 DA A 15 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 7 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 7 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 DA A 15 C3' - O3' - P ANGL. DEV. = 10.8 DEGREES REMARK 500 7 DG A 17 N3 - C4 - N9 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 DG A 17 C6 - C5 - N7 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 DA A 15 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 DA A 15 C3' - O3' - P ANGL. DEV. = 10.0 DEGREES REMARK 500 9 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 9 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 DA A 15 C3' - O3' - P ANGL. DEV. = 13.2 DEGREES REMARK 500 10 DA A 15 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 DA A 15 C3' - O3' - P ANGL. DEV. = 11.3 DEGREES REMARK 500 10 DG A 17 N3 - C4 - N9 ANGL. DEV. = -3.7 DEGREES 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 DG A 5 0.14 SIDE CHAIN REMARK 500 1 DG A 7 0.06 SIDE CHAIN REMARK 500 1 DG A 9 0.07 SIDE CHAIN REMARK 500 1 DT A 10 0.08 SIDE CHAIN REMARK 500 1 DG A 13 0.09 SIDE CHAIN REMARK 500 1 DG A 17 0.06 SIDE CHAIN REMARK 500 1 DG A 18 0.10 SIDE CHAIN REMARK 500 1 DG A 20 0.07 SIDE CHAIN REMARK 500 1 DG A 21 0.06 SIDE CHAIN REMARK 500 1 DT A 23 0.13 SIDE CHAIN REMARK 500 2 DT A 4 0.07 SIDE CHAIN REMARK 500 2 DG A 5 0.14 SIDE CHAIN REMARK 500 2 DG A 9 0.12 SIDE CHAIN REMARK 500 2 DG A 13 0.08 SIDE CHAIN REMARK 500 2 DT A 14 0.09 SIDE CHAIN REMARK 500 2 DG A 18 0.07 SIDE CHAIN REMARK 500 2 DG A 20 0.09 SIDE CHAIN REMARK 500 2 DG A 21 0.08 SIDE CHAIN REMARK 500 3 DG A 5 0.12 SIDE CHAIN REMARK 500 3 DG A 9 0.12 SIDE CHAIN REMARK 500 3 DG A 13 0.08 SIDE CHAIN REMARK 500 3 DG A 17 0.06 SIDE CHAIN REMARK 500 3 DG A 18 0.11 SIDE CHAIN REMARK 500 3 DG A 20 0.11 SIDE CHAIN REMARK 500 3 DT A 23 0.09 SIDE CHAIN REMARK 500 4 DG A 5 0.07 SIDE CHAIN REMARK 500 4 DG A 9 0.10 SIDE CHAIN REMARK 500 4 DG A 12 0.07 SIDE CHAIN REMARK 500 4 DG A 13 0.10 SIDE CHAIN REMARK 500 4 DT A 14 0.08 SIDE CHAIN REMARK 500 4 DG A 18 0.12 SIDE CHAIN REMARK 500 4 DG A 20 0.08 SIDE CHAIN REMARK 500 4 DG A 21 0.05 SIDE CHAIN REMARK 500 4 DT A 23 0.10 SIDE CHAIN REMARK 500 5 DG A 5 0.16 SIDE CHAIN REMARK 500 5 DG A 9 0.11 SIDE CHAIN REMARK 500 5 DG A 12 0.09 SIDE CHAIN REMARK 500 5 DG A 13 0.07 SIDE CHAIN REMARK 500 5 DG A 18 0.09 SIDE CHAIN REMARK 500 5 DG A 20 0.10 SIDE CHAIN REMARK 500 5 DT A 23 0.16 SIDE CHAIN REMARK 500 5 DA A 24 0.06 SIDE CHAIN REMARK 500 6 DT A 4 0.07 SIDE CHAIN REMARK 500 6 DG A 5 0.16 SIDE CHAIN REMARK 500 6 DG A 7 0.07 SIDE CHAIN REMARK 500 6 DG A 9 0.08 SIDE CHAIN REMARK 500 6 DG A 13 0.07 SIDE CHAIN REMARK 500 6 DT A 14 0.06 SIDE CHAIN REMARK 500 6 DG A 18 0.10 SIDE CHAIN REMARK 500 6 DT A 19 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 86 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 26 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 7 O6 REMARK 620 2 DG A 8 O6 90.6 REMARK 620 3 DG A 11 O6 77.9 93.9 REMARK 620 4 DG A 12 O6 142.5 64.9 76.1 REMARK 620 5 DG A 16 O6 105.6 152.3 68.5 89.4 REMARK 620 6 DG A 17 O6 146.5 101.3 131.4 69.7 77.6 REMARK 620 7 DG A 20 O6 65.6 130.0 120.4 151.9 77.7 83.1 REMARK 620 8 DG A 21 O6 91.2 70.4 161.0 105.2 130.0 64.4 67.1 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 27 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 8 O6 REMARK 620 2 DG A 9 O6 72.2 REMARK 620 3 DG A 12 O6 54.8 91.1 REMARK 620 4 DG A 13 O6 119.6 83.4 72.0 REMARK 620 5 DG A 17 O6 93.7 153.9 63.1 85.0 REMARK 620 6 DG A 18 O6 161.8 119.6 133.1 77.1 80.1 REMARK 620 7 DG A 21 O6 66.3 122.8 95.3 151.8 66.9 95.7 REMARK 620 8 DG A 22 O6 93.1 73.3 147.6 131.6 130.6 78.6 71.6 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 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 27 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QUL A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE QUL A 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17379 RELATED DB: BMRB DBREF 2L7V A 4 25 PDB 2L7V 2L7V 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 26 1 HET K A 27 1 HET QUL A 1 51 HET QUL A 2 51 HETNAM K POTASSIUM ION HETNAM QUL N,N-DIETHYL-N'-(10H-INDOLO[3,2-B]QUINOLIN-11-YL)ETHANE- HETNAM 2 QUL 1,2-DIAMINE FORMUL 2 K 2(K 1+) FORMUL 4 QUL 2(C21 H24 N4) LINK O6 DG A 7 K K A 26 1555 1555 2.69 LINK O6 DG A 8 K K A 26 1555 1555 2.81 LINK O6 DG A 8 K K A 27 1555 1555 3.22 LINK O6 DG A 9 K K A 27 1555 1555 2.61 LINK O6 DG A 11 K K A 26 1555 1555 2.73 LINK O6 DG A 12 K K A 26 1555 1555 2.80 LINK O6 DG A 12 K K A 27 1555 1555 3.33 LINK O6 DG A 13 K K A 27 1555 1555 2.59 LINK O6 DG A 16 K K A 26 1555 1555 2.56 LINK O6 DG A 17 K K A 26 1555 1555 2.84 LINK O6 DG A 17 K K A 27 1555 1555 2.76 LINK O6 DG A 18 K K A 27 1555 1555 2.62 LINK O6 DG A 20 K K A 26 1555 1555 2.77 LINK O6 DG A 21 K K A 26 1555 1555 2.95 LINK O6 DG A 21 K K A 27 1555 1555 2.84 LINK O6 DG A 22 K K A 27 1555 1555 2.62 SITE 1 AC1 8 DG A 7 DG A 8 DG A 11 DG A 12 SITE 2 AC1 8 DG A 16 DG A 17 DG A 20 DG A 21 SITE 1 AC2 8 DG A 8 DG A 9 DG A 12 DG A 13 SITE 2 AC2 8 DG A 17 DG A 18 DG A 21 DG A 22 SITE 1 AC3 3 DG A 5 DG A 11 DG A 16 SITE 1 AC4 6 DG A 9 DG A 13 DG A 18 DT A 23 SITE 2 AC4 6 DA A 24 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