HEADER BLOOD CLOTTING, HYDROLASE 11-MAY-22 7V0Z TITLE FACTOR XIA IN COMPLEX WITH COMPOUND 2A COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR XIA LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FXI,PLASMA THROMBOPLASTIN ANTECEDENT,PTA; COMPND 5 EC: 3.4.21.27; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: F11; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS HYDROLASE, SERINE PROTEASE, COAGULATION FACTOR, BLOOD CLOTTING EXPDTA X-RAY DIFFRACTION AUTHOR P.L.SHAFFER,J.SPURLINO,C.M.MILLIGAN REVDAT 3 18-OCT-23 7V0Z 1 REMARK REVDAT 2 24-AUG-22 7V0Z 1 JRNL REVDAT 1 03-AUG-22 7V0Z 0 JRNL AUTH G.XU,Z.LIU,X.WANG,T.LU,R.L.DESJARLAIS,T.THIEU,J.ZHANG, JRNL AUTH 2 Z.H.DEVINE,F.DU,Q.LI,C.M.MILLIGAN,P.SHAFFER,P.E.CEDERVALL, JRNL AUTH 3 J.C.SPURLINO,C.F.STRATTON,B.PIETRAK,L.M.SZEWCZUK,V.WONG, JRNL AUTH 4 R.A.STEELE,W.BRUINZEEL,M.CHINTALA,J.SILVA,M.D.GAUL, JRNL AUTH 5 M.J.MACIELAG,R.NARGUND JRNL TITL DISCOVERY OF POTENT AND ORALLY BIOAVAILABLE PYRIDINE JRNL TITL 2 N-OXIDE-BASED FACTOR XIA INHIBITORS THROUGH EXPLOITING JRNL TITL 3 NONCLASSICAL INTERACTIONS. JRNL REF J.MED.CHEM. V. 65 10419 2022 JRNL REFN ISSN 0022-2623 JRNL PMID 35862732 JRNL DOI 10.1021/ACS.JMEDCHEM.2C00442 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2.4158 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 22980 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.660 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.7000 - 4.3300 1.00 1619 155 0.1583 0.1568 REMARK 3 2 4.3300 - 3.4400 1.00 1550 148 0.1510 0.1760 REMARK 3 3 3.4300 - 3.0000 1.00 1505 141 0.1702 0.1941 REMARK 3 4 3.0000 - 2.7300 1.00 1519 141 0.1980 0.2667 REMARK 3 5 2.7300 - 2.5300 1.00 1521 143 0.1834 0.2053 REMARK 3 6 2.5300 - 2.3800 1.00 1499 144 0.1867 0.2079 REMARK 3 7 2.3800 - 2.2600 1.00 1488 141 0.1793 0.2122 REMARK 3 8 2.2600 - 2.1600 1.00 1491 141 0.2027 0.2339 REMARK 3 9 2.1600 - 2.0800 1.00 1495 142 0.1892 0.2309 REMARK 3 10 2.0800 - 2.0100 1.00 1485 141 0.1734 0.2039 REMARK 3 11 2.0100 - 1.9500 1.00 1489 142 0.1715 0.2065 REMARK 3 12 1.9500 - 1.8900 1.00 1469 139 0.1887 0.2050 REMARK 3 13 1.8900 - 1.8400 1.00 1473 141 0.2184 0.2817 REMARK 3 14 1.8400 - 1.8000 0.93 1386 132 0.2759 0.3308 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 388 THROUGH 624) REMARK 3 ORIGIN FOR THE GROUP (A): 24.2428 -1.9126 -3.8433 REMARK 3 T TENSOR REMARK 3 T11: 0.1337 T22: 0.1394 REMARK 3 T33: 0.1059 T12: -0.0065 REMARK 3 T13: 0.0063 T23: -0.0101 REMARK 3 L TENSOR REMARK 3 L11: 1.6362 L22: 2.0625 REMARK 3 L33: 1.0639 L12: -0.3076 REMARK 3 L13: -0.1582 L23: -0.3844 REMARK 3 S TENSOR REMARK 3 S11: 0.0233 S12: -0.1430 S13: 0.0321 REMARK 3 S21: 0.1078 S22: 0.0245 S23: -0.0033 REMARK 3 S31: -0.0713 S32: 0.0143 S33: -0.0303 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7V0Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265274. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23034 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.70700 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: PHENIX 1.10 REMARK 200 STARTING MODEL: 3SOS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 4000, 100MM NA CITRATE PH 5.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.91250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.62200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.84500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.62200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.91250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.84500 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: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 VAL A 625 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OD1 ASP A 470 O HOH A 801 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 473 -53.74 -124.13 REMARK 500 ASP A 526 -135.94 -152.37 REMARK 500 SER A 594 -63.04 -128.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 7V0Z A 388 625 UNP P03951 FA11_HUMAN 388 625 SEQADV 7V0Z SER A 500 UNP P03951 CYS 500 ENGINEERED MUTATION SEQRES 1 A 238 ILE VAL GLY GLY THR ALA SER VAL ARG GLY GLU TRP PRO SEQRES 2 A 238 TRP GLN VAL THR LEU HIS THR THR SER PRO THR GLN ARG SEQRES 3 A 238 HIS LEU CYS GLY GLY SER ILE ILE GLY ASN GLN TRP ILE SEQRES 4 A 238 LEU THR ALA ALA HIS CYS PHE TYR GLY VAL GLU SER PRO SEQRES 5 A 238 LYS ILE LEU ARG VAL TYR SER GLY ILE LEU ASN GLN SER SEQRES 6 A 238 GLU ILE LYS GLU ASP THR SER PHE PHE GLY VAL GLN GLU SEQRES 7 A 238 ILE ILE ILE HIS ASP GLN TYR LYS MET ALA GLU SER GLY SEQRES 8 A 238 TYR ASP ILE ALA LEU LEU LYS LEU GLU THR THR VAL ASN SEQRES 9 A 238 TYR THR ASP SER GLN ARG PRO ILE SER LEU PRO SER LYS SEQRES 10 A 238 GLY ASP ARG ASN VAL ILE TYR THR ASP CYS TRP VAL THR SEQRES 11 A 238 GLY TRP GLY TYR ARG LYS LEU ARG ASP LYS ILE GLN ASN SEQRES 12 A 238 THR LEU GLN LYS ALA LYS ILE PRO LEU VAL THR ASN GLU SEQRES 13 A 238 GLU CYS GLN LYS ARG TYR ARG GLY HIS LYS ILE THR HIS SEQRES 14 A 238 LYS MET ILE CYS ALA GLY TYR ARG GLU GLY GLY LYS ASP SEQRES 15 A 238 ALA CYS LYS GLY ASP SER GLY GLY PRO LEU SER CYS LYS SEQRES 16 A 238 HIS ASN GLU VAL TRP HIS LEU VAL GLY ILE THR SER TRP SEQRES 17 A 238 GLY GLU GLY CYS ALA GLN ARG GLU ARG PRO GLY VAL TYR SEQRES 18 A 238 THR ASN VAL VAL GLU TYR VAL ASP TRP ILE LEU GLU LYS SEQRES 19 A 238 THR GLN ALA VAL HET OQ6 A 701 40 HETNAM OQ6 METHYL ~{N}-[4-[1-[(1~{R})-1-[5-[5-CHLORANYL-2-(1,2,3, HETNAM 2 OQ6 4-TETRAZOL-1-YL)PHENYL]-1-OXIDANYL-PYRIDIN-2-YL]-2- HETNAM 3 OQ6 CYCLOPROPYL-ETHYL]PYRAZOL-4-YL]PHENYL]CARBAMATE FORMUL 2 OQ6 C28 H25 CL N8 O3 FORMUL 3 HOH *69(H2 O) HELIX 1 AA1 ALA A 429 TYR A 434 5 6 HELIX 2 AA2 SER A 438 LYS A 440 5 3 HELIX 3 AA3 ASN A 450 ILE A 454 5 5 HELIX 4 AA4 MET A 474 GLY A 478 5 5 HELIX 5 AA5 THR A 541 TYR A 549 1 9 HELIX 6 AA6 TYR A 614 GLN A 623 1 10 SHEET 1 AA1 8 THR A 392 ALA A 393 0 SHEET 2 AA1 8 GLN A 533 LYS A 536 -1 O LYS A 534 N THR A 392 SHEET 3 AA1 8 CYS A 514 GLY A 518 -1 N GLY A 518 O GLN A 533 SHEET 4 AA1 8 PRO A 578 HIS A 583 -1 O SER A 580 N TRP A 515 SHEET 5 AA1 8 VAL A 586 TRP A 595 -1 O VAL A 586 N HIS A 583 SHEET 6 AA1 8 GLY A 606 ASN A 610 -1 O VAL A 607 N TRP A 595 SHEET 7 AA1 8 MET A 558 ALA A 561 -1 N ILE A 559 O TYR A 608 SHEET 8 AA1 8 LEU A 539 VAL A 540 -1 N VAL A 540 O CYS A 560 SHEET 1 AA2 6 LEU A 442 SER A 446 0 SHEET 2 AA2 6 GLN A 402 THR A 407 -1 N HIS A 406 O ARG A 443 SHEET 3 AA2 6 ARG A 413 GLY A 422 -1 O LEU A 415 N LEU A 405 SHEET 4 AA2 6 TRP A 425 THR A 428 -1 O LEU A 427 N SER A 419 SHEET 5 AA2 6 ALA A 482 LEU A 486 -1 O ALA A 482 N THR A 428 SHEET 6 AA2 6 VAL A 463 ILE A 468 -1 N ILE A 467 O LEU A 483 SSBOND 1 CYS A 416 CYS A 432 1555 1555 2.04 SSBOND 2 CYS A 514 CYS A 581 1555 1555 2.07 SSBOND 3 CYS A 545 CYS A 560 1555 1555 2.04 SSBOND 4 CYS A 571 CYS A 599 1555 1555 2.04 CISPEP 1 SER A 409 PRO A 410 0 -1.89 CRYST1 59.825 59.690 67.244 90.00 90.00 90.00 P 21 21 21 4 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 0.016715 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014871 0.00000