HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 07-JAN-20 6VFZ TITLE CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL ISOCITRATE DEHYDROGENASE TITLE 2 (IDH2) R140Q MUTANT HOMODIMER IN COMPLEX WITH NADPH AND AG-881 TITLE 3 (VORASIDENIB) INHIBITOR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDH,ICD-M,IDP,NADP(+)-SPECIFIC ICDH,OXALOSUCCINATE COMPND 5 DECARBOXYLASE; COMPND 6 EC: 1.1.1.42; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IDH2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS IDH, ICD-M, IDP, NADP(+)-SPECIFIC ICDH, OXALOSUCCINATE DECARBOXYLASE, KEYWDS 2 OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PADYANA,L.JIN REVDAT 3 11-OCT-23 6VFZ 1 LINK REVDAT 2 04-MAR-20 6VFZ 1 JRNL REVDAT 1 05-FEB-20 6VFZ 0 JRNL AUTH Z.KONTEATIS,E.ARTIN,B.NICOLAY,K.STRALEY,A.K.PADYANA,L.JIN, JRNL AUTH 2 Y.CHEN,R.NARAYARASWAMY,S.TONG,F.WANG,D.ZHOU,D.CUI,Z.CAI, JRNL AUTH 3 Z.LUO,C.FANG,H.TANG,X.LV,R.NAGARAJA,H.YANG,S.M.SU,Z.SUI, JRNL AUTH 4 L.DANG,K.YEN,J.POPOVICI-MULLER,P.CODEGA,C.CAMPOS, JRNL AUTH 5 I.K.MELLINGHOFF,S.A.BILLER JRNL TITL VORASIDENIB (AG-881): A FIRST-IN-CLASS, BRAIN-PENETRANT DUAL JRNL TITL 2 INHIBITOR OF MUTANT IDH1 AND 2 FOR TREATMENT OF GLIOMA. JRNL REF ACS MED.CHEM.LETT. V. 11 101 2020 JRNL REFN ISSN 1948-5875 JRNL PMID 32071674 JRNL DOI 10.1021/ACSMEDCHEMLETT.9B00509 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 61901 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 3046 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 42.0600 - 5.5800 1.00 3004 153 0.1992 0.2016 REMARK 3 2 5.5800 - 4.4300 1.00 2863 136 0.1632 0.1819 REMARK 3 3 4.4300 - 3.8700 1.00 2817 157 0.1513 0.1890 REMARK 3 4 3.8700 - 3.5200 1.00 2810 139 0.1585 0.1775 REMARK 3 5 3.5200 - 3.2600 1.00 2810 143 0.1667 0.1932 REMARK 3 6 3.2600 - 3.0700 1.00 2771 149 0.1728 0.1986 REMARK 3 7 3.0700 - 2.9200 1.00 2789 136 0.1781 0.2257 REMARK 3 8 2.9200 - 2.7900 1.00 2785 127 0.1759 0.2309 REMARK 3 9 2.7900 - 2.6800 1.00 2748 162 0.1778 0.2022 REMARK 3 10 2.6800 - 2.5900 1.00 2797 133 0.1739 0.1994 REMARK 3 11 2.5900 - 2.5100 1.00 2761 145 0.1859 0.2459 REMARK 3 12 2.5100 - 2.4400 1.00 2740 150 0.1825 0.2400 REMARK 3 13 2.4400 - 2.3700 1.00 2755 145 0.1880 0.2247 REMARK 3 14 2.3700 - 2.3200 1.00 2765 143 0.1846 0.2144 REMARK 3 15 2.3200 - 2.2600 1.00 2737 127 0.1884 0.2396 REMARK 3 16 2.2600 - 2.2200 1.00 2743 149 0.1868 0.2178 REMARK 3 17 2.2200 - 2.1700 0.99 2738 139 0.1978 0.2524 REMARK 3 18 2.1700 - 2.1300 0.98 2682 139 0.1996 0.2487 REMARK 3 19 2.1300 - 2.0900 0.93 2540 122 0.1998 0.2734 REMARK 3 20 2.0900 - 2.0600 0.86 2335 133 0.2007 0.2458 REMARK 3 21 2.0600 - 2.0200 0.80 2159 124 0.1963 0.2481 REMARK 3 22 2.0200 - 1.9900 0.62 1706 95 0.2149 0.2176 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) : 0.154 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.741 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.23 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 : 0.004 6905 REMARK 3 ANGLE : 0.680 9368 REMARK 3 CHIRALITY : 0.047 1008 REMARK 3 PLANARITY : 0.005 1224 REMARK 3 DIHEDRAL : 15.475 1011 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -32.4603 11.3263 -25.9006 REMARK 3 T TENSOR REMARK 3 T11: 0.0424 T22: 0.0775 REMARK 3 T33: 0.1006 T12: 0.0094 REMARK 3 T13: 0.0263 T23: -0.0328 REMARK 3 L TENSOR REMARK 3 L11: 1.0312 L22: 1.8490 REMARK 3 L33: 1.7777 L12: 0.5535 REMARK 3 L13: 0.2828 L23: 0.8179 REMARK 3 S TENSOR REMARK 3 S11: -0.1075 S12: 0.0909 S13: 0.0069 REMARK 3 S21: -0.0520 S22: -0.0454 S23: 0.0650 REMARK 3 S31: -0.0847 S32: -0.0832 S33: 0.0621 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 6VFZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246282. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : PILATUS 3 6M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63731 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 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 : 12.70 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.90 REMARK 200 R MERGE FOR SHELL (I) : 0.90500 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 REMARK 200 STARTING MODEL: 5I96 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM CACL2, 0.1M TRIS-HCL PH8.5, 20% REMARK 280 (W/V) PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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 29.53400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.48650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.89850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.48650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.53400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.89850 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: 8850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 TYR A 4 REMARK 465 LEU A 5 REMARK 465 ARG A 6 REMARK 465 VAL A 7 REMARK 465 VAL A 8 REMARK 465 ARG A 9 REMARK 465 SER A 10 REMARK 465 LEU A 11 REMARK 465 CYS A 12 REMARK 465 ARG A 13 REMARK 465 ALA A 14 REMARK 465 SER A 15 REMARK 465 GLY A 16 REMARK 465 SER A 17 REMARK 465 ARG A 18 REMARK 465 PRO A 19 REMARK 465 ALA A 20 REMARK 465 TRP A 21 REMARK 465 ALA A 22 REMARK 465 PRO A 23 REMARK 465 ALA A 24 REMARK 465 ALA A 25 REMARK 465 LEU A 26 REMARK 465 THR A 27 REMARK 465 ALA A 28 REMARK 465 PRO A 29 REMARK 465 THR A 30 REMARK 465 SER A 31 REMARK 465 GLN A 32 REMARK 465 GLU A 33 REMARK 465 GLN A 34 REMARK 465 PRO A 35 REMARK 465 ARG A 36 REMARK 465 ARG A 37 REMARK 465 HIS A 38 REMARK 465 TYR A 39 REMARK 465 ALA A 40 REMARK 465 HIS A 457 REMARK 465 HIS A 458 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 3 REMARK 465 TYR B 4 REMARK 465 LEU B 5 REMARK 465 ARG B 6 REMARK 465 VAL B 7 REMARK 465 VAL B 8 REMARK 465 ARG B 9 REMARK 465 SER B 10 REMARK 465 LEU B 11 REMARK 465 CYS B 12 REMARK 465 ARG B 13 REMARK 465 ALA B 14 REMARK 465 SER B 15 REMARK 465 GLY B 16 REMARK 465 SER B 17 REMARK 465 ARG B 18 REMARK 465 PRO B 19 REMARK 465 ALA B 20 REMARK 465 TRP B 21 REMARK 465 ALA B 22 REMARK 465 PRO B 23 REMARK 465 ALA B 24 REMARK 465 ALA B 25 REMARK 465 LEU B 26 REMARK 465 THR B 27 REMARK 465 ALA B 28 REMARK 465 PRO B 29 REMARK 465 THR B 30 REMARK 465 SER B 31 REMARK 465 GLN B 32 REMARK 465 GLU B 33 REMARK 465 GLN B 34 REMARK 465 PRO B 35 REMARK 465 ARG B 36 REMARK 465 ARG B 37 REMARK 465 HIS B 38 REMARK 465 TYR B 39 REMARK 465 ALA B 40 REMARK 465 ASP B 41 REMARK 465 LYS B 42 REMARK 465 LEU B 449 REMARK 465 GLY B 450 REMARK 465 ARG B 451 REMARK 465 GLN B 452 REMARK 465 HIS B 453 REMARK 465 HIS B 454 REMARK 465 HIS B 455 REMARK 465 HIS B 456 REMARK 465 HIS B 457 REMARK 465 HIS B 458 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 NH2 ARG B 43 OD2 ASP B 76 1.87 REMARK 500 OD1 ASP B 54 O HOH B 601 2.00 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 GLU A 57 -135.05 56.52 REMARK 500 ILE A 71 -65.66 -102.22 REMARK 500 SER A 108 -15.35 78.27 REMARK 500 ALA A 174 51.58 -91.22 REMARK 500 ASP A 177 -135.59 56.50 REMARK 500 LYS A 340 -39.06 -142.07 REMARK 500 SER A 365 72.41 -151.34 REMARK 500 GLU B 57 -128.26 46.62 REMARK 500 ILE B 71 -71.21 -100.30 REMARK 500 SER B 108 -19.13 80.98 REMARK 500 ASP B 177 -136.56 54.28 REMARK 500 ALA B 214 -162.60 -163.28 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 959 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 960 DISTANCE = 6.53 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 CA B 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 291 OD2 REMARK 620 2 ASP B 314 O 87.0 REMARK 620 3 ASP B 314 OD1 87.8 71.3 REMARK 620 4 ASP B 318 OD1 89.3 71.1 142.3 REMARK 620 5 HOH B 696 O 97.8 146.6 141.7 75.9 REMARK 620 6 HOH B 772 O 166.5 88.7 78.7 101.5 92.8 REMARK 620 7 HOH B 778 O 89.8 154.9 83.8 133.8 58.5 88.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 503 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 314 O REMARK 620 2 ASP A 314 OD1 73.0 REMARK 620 3 ASP A 318 OD1 69.5 142.5 REMARK 620 4 HOH A 710 O 148.7 138.1 79.4 REMARK 620 5 HOH A 739 O 145.0 72.6 144.7 65.6 REMARK 620 6 HOH A 884 O 95.0 87.6 95.4 90.7 89.5 REMARK 620 7 ASP B 291 OD2 84.1 86.3 90.0 93.3 87.8 173.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 504 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 317 OG REMARK 620 2 HOH A 832 O 103.3 REMARK 620 3 HOH A 924 O 105.2 130.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 317 OG REMARK 620 2 HOH B 830 O 119.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9UO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NDP A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NDP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VE1 RELATED DB: PDB REMARK 900 6VE1 CONTAINS THE SAME LIGAND COMPLEXED WITH IDH1-R132H REMARK 900 RELATED ID: 6VG0 RELATED DB: PDB DBREF 6VFZ A 1 452 UNP P48735 IDHP_HUMAN 1 452 DBREF 6VFZ B 1 452 UNP P48735 IDHP_HUMAN 1 452 SEQADV 6VFZ GLN A 140 UNP P48735 ARG 140 ENGINEERED MUTATION SEQADV 6VFZ HIS A 453 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS A 454 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS A 455 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS A 456 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS A 457 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS A 458 UNP P48735 EXPRESSION TAG SEQADV 6VFZ GLN B 140 UNP P48735 ARG 140 ENGINEERED MUTATION SEQADV 6VFZ HIS B 453 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS B 454 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS B 455 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS B 456 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS B 457 UNP P48735 EXPRESSION TAG SEQADV 6VFZ HIS B 458 UNP P48735 EXPRESSION TAG SEQRES 1 A 458 MET ALA GLY TYR LEU ARG VAL VAL ARG SER LEU CYS ARG SEQRES 2 A 458 ALA SER GLY SER ARG PRO ALA TRP ALA PRO ALA ALA LEU SEQRES 3 A 458 THR ALA PRO THR SER GLN GLU GLN PRO ARG ARG HIS TYR SEQRES 4 A 458 ALA ASP LYS ARG ILE LYS VAL ALA LYS PRO VAL VAL GLU SEQRES 5 A 458 MET ASP GLY ASP GLU MET THR ARG ILE ILE TRP GLN PHE SEQRES 6 A 458 ILE LYS GLU LYS LEU ILE LEU PRO HIS VAL ASP ILE GLN SEQRES 7 A 458 LEU LYS TYR PHE ASP LEU GLY LEU PRO ASN ARG ASP GLN SEQRES 8 A 458 THR ASP ASP GLN VAL THR ILE ASP SER ALA LEU ALA THR SEQRES 9 A 458 GLN LYS TYR SER VAL ALA VAL LYS CYS ALA THR ILE THR SEQRES 10 A 458 PRO ASP GLU ALA ARG VAL GLU GLU PHE LYS LEU LYS LYS SEQRES 11 A 458 MET TRP LYS SER PRO ASN GLY THR ILE GLN ASN ILE LEU SEQRES 12 A 458 GLY GLY THR VAL PHE ARG GLU PRO ILE ILE CYS LYS ASN SEQRES 13 A 458 ILE PRO ARG LEU VAL PRO GLY TRP THR LYS PRO ILE THR SEQRES 14 A 458 ILE GLY ARG HIS ALA HIS GLY ASP GLN TYR LYS ALA THR SEQRES 15 A 458 ASP PHE VAL ALA ASP ARG ALA GLY THR PHE LYS MET VAL SEQRES 16 A 458 PHE THR PRO LYS ASP GLY SER GLY VAL LYS GLU TRP GLU SEQRES 17 A 458 VAL TYR ASN PHE PRO ALA GLY GLY VAL GLY MET GLY MET SEQRES 18 A 458 TYR ASN THR ASP GLU SER ILE SER GLY PHE ALA HIS SER SEQRES 19 A 458 CYS PHE GLN TYR ALA ILE GLN LYS LYS TRP PRO LEU TYR SEQRES 20 A 458 MET SER THR LYS ASN THR ILE LEU LYS ALA TYR ASP GLY SEQRES 21 A 458 ARG PHE LYS ASP ILE PHE GLN GLU ILE PHE ASP LYS HIS SEQRES 22 A 458 TYR LYS THR ASP PHE ASP LYS ASN LYS ILE TRP TYR GLU SEQRES 23 A 458 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN VAL LEU LYS SEQRES 24 A 458 SER SER GLY GLY PHE VAL TRP ALA CYS LYS ASN TYR ASP SEQRES 25 A 458 GLY ASP VAL GLN SER ASP ILE LEU ALA GLN GLY PHE GLY SEQRES 26 A 458 SER LEU GLY LEU MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 27 A 458 GLY LYS THR ILE GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 28 A 458 THR ARG HIS TYR ARG GLU HIS GLN LYS GLY ARG PRO THR SEQRES 29 A 458 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 30 A 458 GLY LEU GLU HIS ARG GLY LYS LEU ASP GLY ASN GLN ASP SEQRES 31 A 458 LEU ILE ARG PHE ALA GLN MET LEU GLU LYS VAL CYS VAL SEQRES 32 A 458 GLU THR VAL GLU SER GLY ALA MET THR LYS ASP LEU ALA SEQRES 33 A 458 GLY CYS ILE HIS GLY LEU SER ASN VAL LYS LEU ASN GLU SEQRES 34 A 458 HIS PHE LEU ASN THR THR ASP PHE LEU ASP THR ILE LYS SEQRES 35 A 458 SER ASN LEU ASP ARG ALA LEU GLY ARG GLN HIS HIS HIS SEQRES 36 A 458 HIS HIS HIS SEQRES 1 B 458 MET ALA GLY TYR LEU ARG VAL VAL ARG SER LEU CYS ARG SEQRES 2 B 458 ALA SER GLY SER ARG PRO ALA TRP ALA PRO ALA ALA LEU SEQRES 3 B 458 THR ALA PRO THR SER GLN GLU GLN PRO ARG ARG HIS TYR SEQRES 4 B 458 ALA ASP LYS ARG ILE LYS VAL ALA LYS PRO VAL VAL GLU SEQRES 5 B 458 MET ASP GLY ASP GLU MET THR ARG ILE ILE TRP GLN PHE SEQRES 6 B 458 ILE LYS GLU LYS LEU ILE LEU PRO HIS VAL ASP ILE GLN SEQRES 7 B 458 LEU LYS TYR PHE ASP LEU GLY LEU PRO ASN ARG ASP GLN SEQRES 8 B 458 THR ASP ASP GLN VAL THR ILE ASP SER ALA LEU ALA THR SEQRES 9 B 458 GLN LYS TYR SER VAL ALA VAL LYS CYS ALA THR ILE THR SEQRES 10 B 458 PRO ASP GLU ALA ARG VAL GLU GLU PHE LYS LEU LYS LYS SEQRES 11 B 458 MET TRP LYS SER PRO ASN GLY THR ILE GLN ASN ILE LEU SEQRES 12 B 458 GLY GLY THR VAL PHE ARG GLU PRO ILE ILE CYS LYS ASN SEQRES 13 B 458 ILE PRO ARG LEU VAL PRO GLY TRP THR LYS PRO ILE THR SEQRES 14 B 458 ILE GLY ARG HIS ALA HIS GLY ASP GLN TYR LYS ALA THR SEQRES 15 B 458 ASP PHE VAL ALA ASP ARG ALA GLY THR PHE LYS MET VAL SEQRES 16 B 458 PHE THR PRO LYS ASP GLY SER GLY VAL LYS GLU TRP GLU SEQRES 17 B 458 VAL TYR ASN PHE PRO ALA GLY GLY VAL GLY MET GLY MET SEQRES 18 B 458 TYR ASN THR ASP GLU SER ILE SER GLY PHE ALA HIS SER SEQRES 19 B 458 CYS PHE GLN TYR ALA ILE GLN LYS LYS TRP PRO LEU TYR SEQRES 20 B 458 MET SER THR LYS ASN THR ILE LEU LYS ALA TYR ASP GLY SEQRES 21 B 458 ARG PHE LYS ASP ILE PHE GLN GLU ILE PHE ASP LYS HIS SEQRES 22 B 458 TYR LYS THR ASP PHE ASP LYS ASN LYS ILE TRP TYR GLU SEQRES 23 B 458 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN VAL LEU LYS SEQRES 24 B 458 SER SER GLY GLY PHE VAL TRP ALA CYS LYS ASN TYR ASP SEQRES 25 B 458 GLY ASP VAL GLN SER ASP ILE LEU ALA GLN GLY PHE GLY SEQRES 26 B 458 SER LEU GLY LEU MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 27 B 458 GLY LYS THR ILE GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 28 B 458 THR ARG HIS TYR ARG GLU HIS GLN LYS GLY ARG PRO THR SEQRES 29 B 458 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 30 B 458 GLY LEU GLU HIS ARG GLY LYS LEU ASP GLY ASN GLN ASP SEQRES 31 B 458 LEU ILE ARG PHE ALA GLN MET LEU GLU LYS VAL CYS VAL SEQRES 32 B 458 GLU THR VAL GLU SER GLY ALA MET THR LYS ASP LEU ALA SEQRES 33 B 458 GLY CYS ILE HIS GLY LEU SER ASN VAL LYS LEU ASN GLU SEQRES 34 B 458 HIS PHE LEU ASN THR THR ASP PHE LEU ASP THR ILE LYS SEQRES 35 B 458 SER ASN LEU ASP ARG ALA LEU GLY ARG GLN HIS HIS HIS SEQRES 36 B 458 HIS HIS HIS HET 9UO A 501 54 HET NDP A 502 48 HET CA A 503 1 HET NA A 504 1 HET NDP B 501 48 HET CA B 502 1 HET NA B 503 1 HETNAM 9UO 6-(6-CHLOROPYRIDIN-2-YL)-N2,N4-BIS[(2R)-1,1,1- HETNAM 2 9UO TRIFLUOROPROPAN-2-YL]-1,3,5-TRIAZINE-2,4-DIAMINE HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION FORMUL 3 9UO C14 H13 CL F6 N6 FORMUL 4 NDP 2(C21 H30 N7 O17 P3) FORMUL 5 CA 2(CA 2+) FORMUL 6 NA 2(NA 1+) FORMUL 10 HOH *616(H2 O) HELIX 1 AA1 ASP A 56 LEU A 70 1 15 HELIX 2 AA2 GLY A 85 THR A 92 1 8 HELIX 3 AA3 ASP A 94 SER A 108 1 15 HELIX 4 AA4 ASP A 119 LYS A 127 1 9 HELIX 5 AA5 SER A 134 GLY A 144 1 11 HELIX 6 AA6 GLY A 176 ALA A 181 5 6 HELIX 7 AA7 ASP A 225 LYS A 243 1 19 HELIX 8 AA8 ALA A 257 TYR A 274 1 18 HELIX 9 AA9 TYR A 274 ASN A 281 1 8 HELIX 10 AB1 ILE A 290 SER A 300 1 11 HELIX 11 AB2 LYS A 309 PHE A 324 1 16 HELIX 12 AB3 SER A 326 GLY A 328 5 3 HELIX 13 AB4 VAL A 351 LYS A 360 1 10 HELIX 14 AB5 PRO A 368 GLY A 387 1 20 HELIX 15 AB6 ASN A 388 GLY A 409 1 22 HELIX 16 AB7 THR A 412 GLY A 421 1 10 HELIX 17 AB8 ASN A 433 HIS A 456 1 24 HELIX 18 AB9 ASP B 56 LEU B 70 1 15 HELIX 19 AC1 GLY B 85 THR B 92 1 8 HELIX 20 AC2 ASP B 94 SER B 108 1 15 HELIX 21 AC3 ASP B 119 LYS B 127 1 9 HELIX 22 AC4 SER B 134 GLY B 144 1 11 HELIX 23 AC5 GLY B 176 ALA B 181 5 6 HELIX 24 AC6 ASP B 225 LYS B 243 1 19 HELIX 25 AC7 ALA B 257 TYR B 274 1 18 HELIX 26 AC8 TYR B 274 ASN B 281 1 8 HELIX 27 AC9 ILE B 290 SER B 300 1 11 HELIX 28 AD1 LYS B 309 PHE B 324 1 16 HELIX 29 AD2 SER B 326 GLY B 328 5 3 HELIX 30 AD3 VAL B 351 LYS B 360 1 10 HELIX 31 AD4 PRO B 368 GLY B 387 1 20 HELIX 32 AD5 ASN B 388 SER B 408 1 21 HELIX 33 AD6 THR B 412 GLY B 421 1 10 HELIX 34 AD7 LEU B 422 VAL B 425 5 4 HELIX 35 AD8 ASN B 433 ALA B 448 1 16 SHEET 1 AA1 2 ILE A 44 LYS A 45 0 SHEET 2 AA1 2 VAL A 75 ASP A 76 1 O ASP A 76 N ILE A 44 SHEET 1 AA210 LEU A 79 ASP A 83 0 SHEET 2 AA210 VAL A 50 ASP A 54 1 N GLU A 52 O PHE A 82 SHEET 3 AA210 VAL A 109 LYS A 112 1 O VAL A 109 N VAL A 51 SHEET 4 AA210 ILE A 342 ALA A 346 1 O ALA A 344 N LYS A 112 SHEET 5 AA210 MET A 330 VAL A 335 -1 N LEU A 334 O GLU A 343 SHEET 6 AA210 THR A 146 PRO A 151 -1 N THR A 146 O VAL A 335 SHEET 7 AA210 ILE A 168 ARG A 172 -1 O ILE A 170 N ARG A 149 SHEET 8 AA210 PHE A 304 CYS A 308 1 O CYS A 308 N GLY A 171 SHEET 9 AA210 LEU A 246 THR A 250 1 N TYR A 247 O ALA A 307 SHEET 10 AA210 TYR A 285 LEU A 289 1 O ARG A 288 N MET A 248 SHEET 1 AA3 4 THR A 182 ALA A 186 0 SHEET 2 AA3 4 GLY A 216 THR A 224 -1 O GLY A 220 N THR A 182 SHEET 3 AA3 4 GLY B 216 THR B 224 -1 O VAL B 217 N ASN A 223 SHEET 4 AA3 4 THR B 182 ALA B 186 -1 N THR B 182 O GLY B 220 SHEET 1 AA4 4 LYS A 205 PHE A 212 0 SHEET 2 AA4 4 GLY A 190 PRO A 198 -1 N PHE A 192 O TYR A 210 SHEET 3 AA4 4 GLY B 190 PRO B 198 -1 O VAL B 195 N LYS A 193 SHEET 4 AA4 4 LYS B 205 PHE B 212 -1 O TYR B 210 N PHE B 192 SHEET 1 AA5 2 ILE B 44 LYS B 45 0 SHEET 2 AA5 2 VAL B 75 ASP B 76 1 O ASP B 76 N ILE B 44 SHEET 1 AA610 LEU B 79 ASP B 83 0 SHEET 2 AA610 VAL B 50 ASP B 54 1 N ASP B 54 O PHE B 82 SHEET 3 AA610 VAL B 109 LYS B 112 1 O VAL B 111 N MET B 53 SHEET 4 AA610 ILE B 342 ALA B 346 1 O ALA B 344 N LYS B 112 SHEET 5 AA610 MET B 330 VAL B 335 -1 N LEU B 334 O GLU B 343 SHEET 6 AA610 THR B 146 PRO B 151 -1 N THR B 146 O VAL B 335 SHEET 7 AA610 ILE B 168 ARG B 172 -1 O ILE B 170 N ARG B 149 SHEET 8 AA610 PHE B 304 CYS B 308 1 O CYS B 308 N GLY B 171 SHEET 9 AA610 LEU B 246 THR B 250 1 N TYR B 247 O ALA B 307 SHEET 10 AA610 TYR B 285 LEU B 289 1 O ARG B 288 N MET B 248 LINK OD2 ASP A 291 CA CA B 502 1555 1555 2.42 LINK O ASP A 314 CA CA A 503 1555 1555 2.82 LINK OD1 ASP A 314 CA CA A 503 1555 1555 2.30 LINK OG SER A 317 NA NA A 504 1555 1555 2.32 LINK OD1 ASP A 318 CA CA A 503 1555 1555 2.25 LINK CA CA A 503 O HOH A 710 1555 1555 2.36 LINK CA CA A 503 O HOH A 739 1555 1555 2.40 LINK CA CA A 503 O HOH A 884 1555 1555 2.50 LINK CA CA A 503 OD2 ASP B 291 1555 1555 2.38 LINK NA NA A 504 O HOH A 832 1555 1555 3.13 LINK NA NA A 504 O HOH A 924 1555 1555 2.82 LINK O ASP B 314 CA CA B 502 1555 1555 2.89 LINK OD1 ASP B 314 CA CA B 502 1555 1555 2.35 LINK OG SER B 317 NA NA B 503 1555 1555 2.33 LINK OD1 ASP B 318 CA CA B 502 1555 1555 2.34 LINK CA CA B 502 O HOH B 696 1555 1555 2.50 LINK CA CA B 502 O HOH B 772 1555 1555 2.47 LINK CA CA B 502 O HOH B 778 1555 1555 2.30 LINK NA NA B 503 O HOH B 830 1555 1555 2.65 SITE 1 AC1 18 TRP A 164 VAL A 294 VAL A 297 LEU A 298 SITE 2 AC1 18 ASP A 312 VAL A 315 GLN A 316 ILE A 319 SITE 3 AC1 18 LEU A 320 TRP B 164 VAL B 294 VAL B 297 SITE 4 AC1 18 LEU B 298 ASP B 312 VAL B 315 GLN B 316 SITE 5 AC1 18 ILE B 319 LEU B 320 SITE 1 AC2 24 LYS A 112 ALA A 114 THR A 115 ILE A 116 SITE 2 AC2 24 THR A 117 ARG A 122 ASN A 136 GLU A 345 SITE 3 AC2 24 HIS A 348 GLY A 349 THR A 350 VAL A 351 SITE 4 AC2 24 THR A 352 ARG A 353 HIS A 354 THR A 366 SITE 5 AC2 24 ASN A 367 HOH A 676 HOH A 709 HOH A 743 SITE 6 AC2 24 HOH A 748 HOH A 750 HOH A 756 HOH A 776 SITE 1 AC3 6 ASP A 314 ASP A 318 HOH A 710 HOH A 739 SITE 2 AC3 6 HOH A 884 ASP B 291 SITE 1 AC4 4 ARG A 149 ILE A 170 SER A 317 HOH A 924 SITE 1 AC5 21 LYS B 112 THR B 115 ILE B 116 THR B 117 SITE 2 AC5 21 ARG B 122 ASN B 136 GLU B 345 HIS B 348 SITE 3 AC5 21 GLY B 349 THR B 350 VAL B 351 THR B 352 SITE 4 AC5 21 ARG B 353 HIS B 354 THR B 366 ASN B 367 SITE 5 AC5 21 HOH B 650 HOH B 668 HOH B 725 HOH B 733 SITE 6 AC5 21 HOH B 777 SITE 1 AC6 6 ASP A 291 ASP B 314 ASP B 318 HOH B 696 SITE 2 AC6 6 HOH B 772 HOH B 778 SITE 1 AC7 4 ARG B 149 ILE B 170 SER B 317 HOH B 830 CRYST1 59.068 119.797 130.973 90.00 90.00 90.00 P 21 21 21 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 0.016930 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007635 0.00000