HEADER HIV-1 18-DEC-03 1UUD TITLE NMR STRUCTURE OF A SYNTHETIC SMALL MOLECULE, RBT203, BOUND TITLE 2 TO HIV-1 TAR RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-(*GP*GP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP COMPND 3 *CP*CP*UP*GP*GP*GP*AP*GP*CP*UP*CP*UP*CP*UP*GP*CP*C) -3'); COMPND 4 CHAIN: B; COMPND 5 SYNONYM: HIV-1 TAR RNA; COMPND 6 OTHER_DETAILS: BULGED STEM LOOP REGION FROM 5'LTR OF HIV-1 COMPND 7 MRNA-BINDING SITE FOR TRANSCRIPTIONAL ACTIVATOR PROTEIN COMPND 8 TAT. SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1 (CLONE SOURCE 4 12); SOURCE 5 ORGANISM_COMMON: HIV-1; SOURCE 6 ORGANISM_TAXID: 11706; SOURCE 7 OTHER_DETAILS: 29 NUCLEOTIDE SEQUENCE COMPRISING PRIMARY SOURCE 8 BINDING SITE OF HIV-1 TAT, SYNTHESIZED USING T7 RNA SOURCE 9 POLYMERASE OFF OF A DNA TEMPLATE KEYWDS HIV-1, TAR RNA, DRUG DESIGN, LIGAND-RNA INTERACTION, RNA KEYWDS 2 BULGE EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR B.DAVIS,M.AFSHAR,G.VARANI,J.KARN,A.I.H.MURCHIE,G.LENTZEN, AUTHOR 2 M.J.DRYSDALE,A.J.POTTER,J.BOWER,F.ABOUL-ELA REVDAT 2 24-FEB-09 1UUD 1 VERSN REVDAT 1 15-MAR-04 1UUD 0 JRNL AUTH B.DAVIS,M.AFSHAR,G.VARANI,A.I.H.MURCHIE,J.KARN, JRNL AUTH 2 G.LENTZEN,M.J.DRYSDALE,J.BOWER,A.J.POTTER, JRNL AUTH 3 F.ABOUL-ELA JRNL TITL RATIONAL DESIGN OF INHIBITORS OF HIV-1 TAR RNA JRNL TITL 2 THROUGH THE STABILISATION OF ELECTROSTATIC "HOT JRNL TITL 3 SPOTS" JRNL REF J.MOL.BIOL. V. 336 343 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 14757049 JRNL DOI 10.1016/J.JMB.2003.12.046 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.ABOUL-ELA,J.JKARN,G.VARANI REMARK 1 TITL THE STRUCTURE OF THE HUMAN IMMUNODEFICIENCY VIRUS REMARK 1 TITL 2 RECOGNITION BY TAT PROTEIN REMARK 1 REF J.MOL.BIOL. V. 253 313 1995 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 7563092 REMARK 1 DOI 10.1006/JMBI.1995.0555 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT INCLUDED A NUMBER OF REMARK 3 MODELLING CONSTRAINTS BASED UPON PREVIOUSLY PUBLISHED DATA, AS REMARK 3 WELL AS FINAL GENTLE REFINEMENT STEP USING CHARMM. DETAILS CAN REMARK 3 BE FOUND IN THE JOURNAL CITATION ABOVE REMARK 4 REMARK 4 1UUD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-03. REMARK 100 THE PDBE ID CODE IS EBI-14236. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : 20 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, COSY, ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800; 600; 600; 500 REMARK 210 SPECTROMETER MODEL : DRX800; DRX600; DMX600; REMARK 210 AMX500 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR/CHARMM REMARK 210 METHOD USED : NOE-RESTRAINED DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRRAINT REMARK 210 VIOLATION ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR NMR REMARK 210 SPECTROSCOPY, DETECTING INTERMOLECULAR NOES. RNA REMARK 210 INTRAMOLECULAR RESTRAINTS WERE AS IN ABOUL-ELA ET AL, JMB REMARK 210 1995, AS THE NMR SPECTRA FOR THE RNA AS ABOUND BY THE REMARK 210 LIGAND RBT203 SHOWED SIMILAR NOE AND CHEMICAL SHIFT REMARK 210 PATTERNS TO THE LATTER 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 G B 17 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G B 17 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G B 18 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G B 18 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 A B 20 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G B 21 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G B 21 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 A B 22 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G B 26 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G B 26 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 A B 27 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 G B 28 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G B 28 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 32 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G B 32 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G B 33 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G B 33 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 G B 34 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 G B 34 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 A B 35 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G B 36 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G B 36 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 G B 43 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 G B 43 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES 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 P14 B1046 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UTS RELATED DB: PDB REMARK 900 DESIGNED HIV-1 TAR BINDING LIGAND REMARK 900 RELATED ID: 1UUI RELATED DB: PDB REMARK 900 DESIGNED HIV-1 TAR BINDING LIGAND DBREF 1UUD B 17 45 PDB 1UUD 1UUD 17 45 SEQRES 1 B 29 G G C A G A U C U G A G C SEQRES 2 B 29 C U G G G A G C U C U C U SEQRES 3 B 29 G C C HET P14 B1046 57 HETNAM P14 N-[2-(2-{[(4-{[AMINO(IMINO)METHYL]AMINO} HETNAM 2 P14 BUTYL)AMINO]METHYL}-4-METHOXYPHENOXY)ETHYL] HETNAM 3 P14 GUANIDINE HETSYN P14 RBT203 INHIBITOR FORMUL 2 P14 C16 H31 N7 O2 SITE 1 AC1 9 A B 22 U B 23 G B 26 A B 27 SITE 2 AC1 9 G B 28 A B 35 G B 36 C B 37 SITE 3 AC1 9 U B 38 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