HEADER HYDROLASE/INHIBITOR 17-JAN-23 8FUI TITLE HIV-1 WILD TYPE PROTEASE WITH GRL-02519A, WITH N-(2,5-DIMETHYLPHENYL)- TITLE 2 4-(PYRIDIN-3-YL)PYRIMIDIN-2-AMINE AS P2-P3 GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: ISOLATE BRU/LAI; SOURCE 5 GENE: POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJ414 KEYWDS ASPARTIC ACID PROTEASE, HIV-1 PROTEASE, INHIBITORS, KEYWDS 2 PYRIDYLPYRIMIDINE, HYDROLASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-F.WANG,A.E.WONG-SAM,A.K.GHOSH,I.T.WEBER REVDAT 2 22-MAY-24 8FUI 1 REMARK REVDAT 1 24-MAY-23 8FUI 0 JRNL AUTH A.K.GHOSH,J.L.MISHEVICH,S.KOVELA,R.SHAKTAH,A.K.GHOSH, JRNL AUTH 2 M.JOHNSON,Y.F.WANG,A.WONG-SAM,J.AGNISWAMY,M.AMANO, JRNL AUTH 3 Y.TAKAMATSU,S.I.HATTORI,I.T.WEBER,H.MITSUYA JRNL TITL EXPLORATION OF IMATINIB AND NILOTINIB-DERIVED TEMPLATES AS JRNL TITL 2 THE P2-LIGAND FOR HIV-1 PROTEASE INHIBITORS: DESIGN, JRNL TITL 3 SYNTHESIS, PROTEIN X-RAY STRUCTURAL STUDIES, AND BIOLOGICAL JRNL TITL 4 EVALUATION. JRNL REF EUR.J.MED.CHEM. V. 255 15385 2023 JRNL REFN ISSN 0223-5234 JRNL PMID 37150084 JRNL DOI 10.1016/J.EJMECH.2023.115385 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 56906 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3079 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2069 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 46.24 REMARK 3 BIN R VALUE (WORKING SET) : 0.3410 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1512 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : -1.08000 REMARK 3 B33 (A**2) : 1.57000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.042 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.514 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1882 ; 0.012 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1884 ; 0.007 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2602 ; 1.764 ; 1.713 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4414 ; 0.671 ; 1.614 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 254 ; 7.019 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 8 ; 5.363 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 341 ;12.550 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 306 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2117 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 363 ; 0.019 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 891 ; 2.436 ; 1.474 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 892 ; 2.435 ; 1.477 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1132 ; 3.108 ; 2.220 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1133 ; 3.108 ; 2.222 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 991 ; 5.967 ; 1.928 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 988 ; 5.973 ; 1.924 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1448 ; 5.998 ; 2.710 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1974 ; 6.505 ;23.935 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1912 ; 6.506 ;21.189 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3766 ;18.096 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8FUI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000269538. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60036 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 50.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.38300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 4.064 REMARK 200 STARTING MODEL: 3NU3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.1 M NACL, 0.1 M SODIUM ACETATE, PH REMARK 280 5.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 29.22550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.06800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.22550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.06800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL 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: 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 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 8 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 423 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH B 327 DISTANCE = 6.00 ANGSTROMS 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 NA A 202 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 60 O REMARK 620 2 HOH A 328 O 94.1 REMARK 620 3 HOH A 345 O 101.8 78.3 REMARK 620 4 HOH A 346 O 91.1 88.2 161.9 REMARK 620 5 HOH A 372 O 78.8 172.5 100.6 94.4 REMARK 620 6 HOH A 386 O 169.5 91.2 88.1 80.1 96.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 60 O REMARK 620 2 HOH B 213 O 98.4 REMARK 620 3 HOH B 221 O 112.3 74.3 REMARK 620 4 HOH B 249 O 69.5 167.9 110.1 REMARK 620 5 HOH B 268 O 165.4 82.6 82.1 108.9 REMARK 620 6 HOH B 294 O 91.2 78.8 146.3 100.4 74.6 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8FUJ RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH GRL-03419A, N-(2,5-DIMETHYLPHENYL)-4- REMARK 900 (PYRIDIN-3-YL)PYRIMIDIN-2-AMINE AS P2-P3 GROUP AND 3,5- REMARK 900 DIFLUOROPHENYLMETHYL AS THE P1 GROUP REMARK 900 RELATED ID: 2IEN RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH DARUNAVIR, BI-THF AS THE P2 GREOUP REMARK 900 RELATED ID: 4ZIP RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH GRL-0648A, N-(2,5-DIMETHYLOXAZOL-4-YL) REMARK 900 METHYL)-N,3,5-TRIMETHYL)BENZAMIDE AS THE P2-P3 GROUP REMARK 900 RELATED ID: 5UPZ RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH GRL-0518A, N,3-DIMETHYL-N-((4- REMARK 900 METHYLOXAZOL-2-YL)METHYL)BENZAMIDE AS THE P2-P3 GROUP REMARK 900 RELATED ID: 5UOV RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH GRL-1118A, (R)-(2-(4-METHYLTHIAZOL-2- REMARK 900 YL)PYRROLIDIN-1-YL)(M-TOLYL)METHANONE AS THE P2-P3 GROUP REMARK 900 RELATED ID: 6DV0 RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH GRL-02815A, TERT-BUTYL(S)-(6- REMARK 900 METHYLTHIOCHROMAN-4-YL)CARBAMATE AS THE P2-P3 GROUP REMARK 900 RELATED ID: 6DV4 RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH GRL-04315A, TERT-BUTYL((1R,4S)-4- REMARK 900 HYDROXY-7-METHYL-1,2,3,4-TETRAHYDRONAPHTHALEN-1-YL)CARBAMATE AS THE REMARK 900 P2-P3 GROUP DBREF 8FUI A 1 99 UNP Q5RZ08 Q5RZ08_9HIV1 1 99 DBREF 8FUI B 1 99 UNP Q5RZ08 Q5RZ08_9HIV1 1 99 SEQADV 8FUI LYS A 7 UNP Q5RZ08 GLN 7 ENGINEERED MUTATION SEQADV 8FUI ILE A 33 UNP Q5RZ08 LEU 33 ENGINEERED MUTATION SEQADV 8FUI ILE A 63 UNP Q5RZ08 LEU 63 ENGINEERED MUTATION SEQADV 8FUI ALA A 67 UNP Q5RZ08 CYS 67 ENGINEERED MUTATION SEQADV 8FUI ALA A 95 UNP Q5RZ08 CYS 95 ENGINEERED MUTATION SEQADV 8FUI LYS B 7 UNP Q5RZ08 GLN 7 ENGINEERED MUTATION SEQADV 8FUI ILE B 33 UNP Q5RZ08 LEU 33 ENGINEERED MUTATION SEQADV 8FUI ILE B 63 UNP Q5RZ08 LEU 63 ENGINEERED MUTATION SEQADV 8FUI ALA B 67 UNP Q5RZ08 CYS 67 ENGINEERED MUTATION SEQADV 8FUI ALA B 95 UNP Q5RZ08 CYS 95 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 A 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 B 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 B 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 B 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 B 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY ALA THR LEU ASN PHE HET Y9R A 201 98 HET NA A 202 1 HET CL A 203 1 HET ACT A 204 4 HET GOL A 205 6 HET FMT A 206 3 HET NA B 101 1 HET CL B 102 1 HET CL B 103 1 HET CL B 104 1 HET FMT B 105 3 HETNAM Y9R N-{(2S,3R)-4-[(4-AMINOBENZENE-1-SULFONYL)(2- HETNAM 2 Y9R METHYLPROPYL)AMINO]-3-HYDROXY-1-PHENYLBUTAN-2-YL}-4- HETNAM 3 Y9R METHYL-3-{[(4P)-4-(PYRIDIN-3-YL)PYRIMIDIN-2- HETNAM 4 Y9R YL]AMINO}BENZAMIDE HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM FMT FORMIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 Y9R C37 H41 N7 O4 S FORMUL 4 NA 2(NA 1+) FORMUL 5 CL 4(CL 1-) FORMUL 6 ACT C2 H3 O2 1- FORMUL 7 GOL C3 H8 O3 FORMUL 8 FMT 2(C H2 O2) FORMUL 14 HOH *250(H2 O) HELIX 1 AA1 GLY A 86 THR A 91 1 6 HELIX 2 AA2 GLN A 92 GLY A 94 5 3 HELIX 3 AA3 GLY B 86 THR B 91 1 6 SHEET 1 AA1 4 GLN A 2 ILE A 3 0 SHEET 2 AA1 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 AA1 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 96 SHEET 4 AA1 4 GLN B 2 ILE B 3 -1 O ILE B 3 N LEU A 97 SHEET 1 AA2 8 TRP A 42 GLY A 49 0 SHEET 2 AA2 8 GLY A 52 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 AA2 8 HIS A 69 VAL A 77 -1 O ALA A 71 N ILE A 64 SHEET 4 AA2 8 THR A 31 ILE A 33 1 N ILE A 33 O LEU A 76 SHEET 5 AA2 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 AA2 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 AA2 8 LEU A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 AA2 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 AA3 8 LYS B 43 GLY B 49 0 SHEET 2 AA3 8 GLY B 52 ILE B 66 -1 O GLN B 58 N LYS B 43 SHEET 3 AA3 8 HIS B 69 VAL B 77 -1 O HIS B 69 N ILE B 66 SHEET 4 AA3 8 VAL B 32 ILE B 33 1 N ILE B 33 O LEU B 76 SHEET 5 AA3 8 ILE B 84 ILE B 85 -1 O ILE B 84 N VAL B 32 SHEET 6 AA3 8 GLN B 18 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 AA3 8 LEU B 10 ILE B 15 -1 N ILE B 13 O LYS B 20 SHEET 8 AA3 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 LINK O ASP A 60 NA NA A 202 1555 1555 2.38 LINK NA NA A 202 O HOH A 328 1555 1555 2.44 LINK NA NA A 202 O HOH A 345 1555 1555 2.35 LINK NA NA A 202 O HOH A 346 1555 1555 2.43 LINK NA NA A 202 O HOH A 372 1555 1555 2.37 LINK NA NA A 202 O HOH A 386 1555 1555 2.64 LINK O ASP B 60 NA NA B 101 1555 1555 2.50 LINK NA NA B 101 O HOH B 213 1555 1555 2.67 LINK NA NA B 101 O HOH B 221 1555 1555 2.25 LINK NA NA B 101 O HOH B 249 1555 1555 2.55 LINK NA NA B 101 O AHOH B 268 1555 1555 3.09 LINK NA NA B 101 O HOH B 294 1555 1555 2.38 CRYST1 58.451 86.136 46.113 90.00 90.00 90.00 P 21 21 2 8 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 0.017108 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011610 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021686 0.00000