HEADER INHIBITOR 27-NOV-15 5FP7 TITLE CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4-METHYLTHIOPHEN-2- TITLE 2 YL METHYLAMINOPYRIDINE-4-CARBOXYLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 11-341; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2D, HUMAN LYSINE-SPECIFIC COMPND 7 DEMETHYLASE 4D, JMJD2D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, LYSINE SPECIFIC HISTONE DEMETHYLASE, JMJD2D, KDM4D, KEYWDS 2 JUMONJI EXPDTA X-RAY DIFFRACTION AUTHOR C.CHUNG REVDAT 2 16-JAN-19 5FP7 1 JRNL REVDAT 1 09-NOV-16 5FP7 0 JRNL AUTH S.M.WESTAWAY,A.G.PRESTON,M.D.BARKER,F.BROWN,J.A.BROWN, JRNL AUTH 2 M.CAMPBELL,C.W.CHUNG,G.DREWES,R.EAGLE,N.GARTON,L.GORDON, JRNL AUTH 3 C.HASLAM,T.G.HAYHOW,P.G.HUMPHREYS,G.JOBERTY,R.KATSO, JRNL AUTH 4 L.KRUIDENIER,M.LEVERIDGE,M.PEMBERTON,I.RIOJA,G.A.SEAL, JRNL AUTH 5 T.SHIPLEY,O.SINGH,C.J.SUCKLING,J.TAYLOR,P.THOMAS,D.M.WILSON, JRNL AUTH 6 K.LEE,R.K.PRINJHA JRNL TITL CELL PENETRANT INHIBITORS OF THE KDM4 AND KDM5 FAMILIES OF JRNL TITL 2 HISTONE LYSINE DEMETHYLASES. 2. JRNL TITL 3 PYRIDO[3,4-D]PYRIMIDIN-4(3H)-ONE DERIVATIVES. JRNL REF J. MED. CHEM. V. 59 1370 2016 JRNL REFN ISSN 1520-4804 JRNL PMID 26771203 JRNL DOI 10.1021/ACS.JMEDCHEM.5B01538 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 25647 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1356 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1680 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2687 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 456 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.53000 REMARK 3 B22 (A**2) : 0.53000 REMARK 3 B33 (A**2) : -1.06000 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): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.360 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2896 ; 0.006 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1989 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3931 ; 1.092 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4811 ; 0.805 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 5.506 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;34.545 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 468 ;12.266 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;18.255 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 399 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3230 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 643 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 11 A 340 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2785 3.5083 18.5897 REMARK 3 T TENSOR REMARK 3 T11: 0.0073 T22: 0.0110 REMARK 3 T33: 0.0156 T12: -0.0058 REMARK 3 T13: -0.0021 T23: 0.0104 REMARK 3 L TENSOR REMARK 3 L11: 0.3611 L22: 0.1986 REMARK 3 L33: 0.3751 L12: -0.0629 REMARK 3 L13: 0.1439 L23: 0.0367 REMARK 3 S TENSOR REMARK 3 S11: 0.0375 S12: -0.0196 S13: 0.0015 REMARK 3 S21: 0.0114 S22: -0.0302 S23: -0.0175 REMARK 3 S31: 0.0430 S32: -0.0237 S33: -0.0073 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 5FP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1290065661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SATURN A200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25133 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 26.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.4, 2.3M AMMONIUM REMARK 280 SULPHATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 75.29500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.70500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.94250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.70500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.64750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.70500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.94250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.70500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.70500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.64750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.29500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A1350 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2012 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2278 LIES ON A SPECIAL POSITION. 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 GLY A 8 REMARK 465 HIS A 9 REMARK 465 MET A 10 REMARK 465 ASP A 341 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 ASN A 202 O HOH A 2327 2.06 REMARK 500 NH2 ARG A 236 O HOH A 2366 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 221 CD GLN A 221 OE1 -0.220 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 GLN A 221 OE1 - CD - NE2 ANGL. DEV. = -16.6 DEGREES 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 186 -10.00 77.46 REMARK 500 LYS A 186 -10.03 77.46 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 TYR A 179 0.10 SIDE CHAIN 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 A2002 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A2199 DISTANCE = 6.18 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 ZN A 350 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 244 NE2 REMARK 620 2 CYS A 312 SG 98.5 REMARK 620 3 CYS A 238 SG 113.4 114.7 REMARK 620 4 CYS A 310 SG 106.6 104.0 117.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 360 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 HOH A2312 O 87.3 REMARK 620 3 HOH A2317 O 175.6 92.8 REMARK 620 4 HIS A 280 NE2 86.6 168.6 94.0 REMARK 620 5 GLU A 194 OE2 98.7 84.7 85.7 86.7 REMARK 620 6 YC8 A1344 N1 92.6 91.0 83.0 98.9 167.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YC8 A 1344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1347 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1348 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1349 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1350 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1351 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FP3 RELATED DB: PDB REMARK 900 CELL PENETRANT INHIBITORS OF THE JMJD2 (KDM4) AND JARID1 (KDM5) REMARK 900 FAMILIES OF HISTONE LYSINE DEMETHYLASES REMARK 900 RELATED ID: 5FP4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-( 4- REMARK 900 PHENYLBUTANAMIDO)PYRIDINE-4-CARBOXYLIC ACID REMARK 900 RELATED ID: 5FP8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3-4 - REMARK 900 METHYLTHIOPHEN-2-YLMETHYLAMINOPYRIDINE-4-CARBOXYLIC ACID REMARK 900 RELATED ID: 5FP9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3- AMINOPYRIDINE-4- REMARK 900 CARBOXYLIC ACID REMARK 900 RELATED ID: 5FPA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 3H, 4H-PYRIDO-3,4- REMARK 900 D-PYRIMIDIN-4-ONE REMARK 900 RELATED ID: 5FPB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN KDM4D IN COMPLEX WITH 2- 1H-PYRAZOL-4- REMARK 900 YLOXY-3H,4H-PYRIDO-3,4-D-PYRIMIDIN- 4-ONE DBREF 5FP7 A 11 341 UNP Q6B0I6 KDM4D_HUMAN 11 341 SEQADV 5FP7 GLY A 8 UNP Q6B0I6 EXPRESSION TAG SEQADV 5FP7 HIS A 9 UNP Q6B0I6 EXPRESSION TAG SEQADV 5FP7 MET A 10 UNP Q6B0I6 EXPRESSION TAG SEQRES 1 A 334 GLY HIS MET ALA GLN ASN PRO ASN CYS ASN ILE MET ILE SEQRES 2 A 334 PHE HIS PRO THR LYS GLU GLU PHE ASN ASP PHE ASP LYS SEQRES 3 A 334 TYR ILE ALA TYR MET GLU SER GLN GLY ALA HIS ARG ALA SEQRES 4 A 334 GLY LEU ALA LYS ILE ILE PRO PRO LYS GLU TRP LYS ALA SEQRES 5 A 334 ARG GLU THR TYR ASP ASN ILE SER GLU ILE LEU ILE ALA SEQRES 6 A 334 THR PRO LEU GLN GLN VAL ALA SER GLY ARG ALA GLY VAL SEQRES 7 A 334 PHE THR GLN TYR HIS LYS LYS LYS LYS ALA MET THR VAL SEQRES 8 A 334 GLY GLU TYR ARG HIS LEU ALA ASN SER LYS LYS TYR GLN SEQRES 9 A 334 THR PRO PRO HIS GLN ASN PHE GLU ASP LEU GLU ARG LYS SEQRES 10 A 334 TYR TRP LYS ASN ARG ILE TYR ASN SER PRO ILE TYR GLY SEQRES 11 A 334 ALA ASP ILE SER GLY SER LEU PHE ASP GLU ASN THR LYS SEQRES 12 A 334 GLN TRP ASN LEU GLY HIS LEU GLY THR ILE GLN ASP LEU SEQRES 13 A 334 LEU GLU LYS GLU CYS GLY VAL VAL ILE GLU GLY VAL ASN SEQRES 14 A 334 THR PRO TYR LEU TYR PHE GLY MET TRP LYS THR THR PHE SEQRES 15 A 334 ALA TRP HIS THR GLU ASP MET ASP LEU TYR SER ILE ASN SEQRES 16 A 334 TYR LEU HIS LEU GLY GLU PRO LYS THR TRP TYR VAL VAL SEQRES 17 A 334 PRO PRO GLU HIS GLY GLN ARG LEU GLU ARG LEU ALA ARG SEQRES 18 A 334 GLU LEU PHE PRO GLY SER SER ARG GLY CYS GLY ALA PHE SEQRES 19 A 334 LEU ARG HIS LYS VAL ALA LEU ILE SER PRO THR VAL LEU SEQRES 20 A 334 LYS GLU ASN GLY ILE PRO PHE ASN ARG ILE THR GLN GLU SEQRES 21 A 334 ALA GLY GLU PHE MET VAL THR PHE PRO TYR GLY TYR HIS SEQRES 22 A 334 ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA GLU ALA ILE SEQRES 23 A 334 ASN PHE ALA THR PRO ARG TRP ILE ASP TYR GLY LYS MET SEQRES 24 A 334 ALA SER GLN CYS SER CYS GLY GLU ALA ARG VAL THR PHE SEQRES 25 A 334 SER MET ASP ALA PHE VAL ARG ILE LEU GLN PRO GLU ARG SEQRES 26 A 334 TYR ASP LEU TRP LYS ARG GLY GLN ASP HET ZN A 350 1 HET FE2 A 360 1 HET GOL A1341 6 HET GOL A1342 6 HET GOL A1343 6 HET YC8 A1344 21 HET SO4 A1345 5 HET SO4 A1346 5 HET SO4 A1347 5 HET SO4 A1348 5 HET SO4 A1349 5 HET SO4 A1350 5 HET SO4 A1351 5 HETNAM ZN ZINC ION HETNAM FE2 FE (II) ION HETNAM GOL GLYCEROL HETNAM YC8 3-(4-PHENYLBUTANOYLAMINO)PYRIDINE-4-CARBOXYLIC ACID HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 FE2 FE 2+ FORMUL 4 GOL 3(C3 H8 O3) FORMUL 7 YC8 C16 H16 N2 O3 FORMUL 8 SO4 7(O4 S 2-) FORMUL 15 HOH *456(H2 O) HELIX 1 1 GLU A 26 ASN A 29 5 4 HELIX 2 2 ASP A 30 GLN A 41 1 12 HELIX 3 3 GLY A 42 ALA A 46 5 5 HELIX 4 4 VAL A 98 ASN A 106 1 9 HELIX 5 5 ASN A 117 ARG A 129 1 13 HELIX 6 6 ILE A 130 ASN A 132 5 3 HELIX 7 7 THR A 159 GLY A 169 1 11 HELIX 8 8 GLU A 194 LEU A 198 5 5 HELIX 9 9 PRO A 216 GLU A 218 5 3 HELIX 10 10 HIS A 219 PHE A 231 1 13 HELIX 11 11 PHE A 231 CYS A 238 1 8 HELIX 12 12 ALA A 240 LYS A 245 5 6 HELIX 13 13 SER A 250 ASN A 257 1 8 HELIX 14 14 THR A 297 ARG A 299 5 3 HELIX 15 15 TRP A 300 ALA A 307 1 8 HELIX 16 16 SER A 320 GLN A 329 1 10 HELIX 17 17 GLN A 329 GLN A 340 1 12 SHEET 1 AA10 MET A 19 PHE A 21 0 SHEET 2 AA10 LEU A 48 ILE A 51 1 O LEU A 48 N MET A 19 SHEET 3 AA10 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 AA10 TYR A 199 GLY A 207 -1 O SER A 200 N THR A 274 SHEET 5 AA10 ASN A 288 PHE A 295 -1 O CYS A 289 N HIS A 205 SHEET 6 AA10 TYR A 179 GLY A 183 -1 O TYR A 179 N ALA A 292 SHEET 7 AA10 ILE A 135 SER A 141 -1 O GLY A 137 N PHE A 182 SHEET 8 AA10 LEU A 75 ARG A 82 -1 O LEU A 75 N TYR A 136 SHEET 9 AA10 VAL A 85 LYS A 92 -1 O VAL A 85 N ARG A 82 SHEET 10 AA10 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 AB 2 LEU A 70 ILE A 71 0 SHEET 2 AB 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 AC 4 THR A 188 HIS A 192 0 SHEET 2 AC 4 TYR A 279 ASN A 284 -1 O HIS A 280 N HIS A 192 SHEET 3 AC 4 LYS A 210 VAL A 215 -1 O THR A 211 N PHE A 283 SHEET 4 AC 4 ASN A 262 GLN A 266 -1 O ASN A 262 N VAL A 214 LINK ZN ZN A 350 NE2 HIS A 244 1555 1555 2.04 LINK ZN ZN A 350 SG CYS A 312 1555 1555 2.35 LINK ZN ZN A 350 SG CYS A 238 1555 1555 2.18 LINK ZN ZN A 350 SG CYS A 310 1555 1555 2.24 LINK FE FE2 A 360 NE2 HIS A 192 1555 1555 2.23 LINK FE FE2 A 360 O HOH A2312 1555 1555 2.22 LINK FE FE2 A 360 O HOH A2317 1555 1555 2.23 LINK FE FE2 A 360 NE2 HIS A 280 1555 1555 2.16 LINK FE FE2 A 360 OE2 GLU A 194 1555 1555 2.13 LINK FE FE2 A 360 N1 YC8 A1344 1555 1555 2.11 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 6 HIS A 192 GLU A 194 HIS A 280 YC8 A1344 SITE 2 AC2 6 HOH A2312 HOH A2317 SITE 1 AC3 8 PHE A 21 HIS A 22 GLU A 27 TYR A 34 SITE 2 AC3 8 TYR A 37 HOH A2036 HOH A2044 HOH A2452 SITE 1 AC4 5 PHE A 31 LYS A 150 TRP A 152 ASN A 153 SITE 2 AC4 5 HOH A2062 SITE 1 AC5 6 PHE A 118 ARG A 263 ILE A 264 THR A 265 SITE 2 AC5 6 HOH A2398 HOH A2453 SITE 1 AC6 15 LEU A 75 HIS A 90 TYR A 136 ASP A 139 SITE 2 AC6 15 PHE A 189 HIS A 192 ASN A 202 LYS A 210 SITE 3 AC6 15 TRP A 212 LYS A 245 HIS A 280 FE2 A 360 SITE 4 AC6 15 HOH A2165 HOH A2312 HOH A2317 SITE 1 AC7 6 PRO A 113 LYS A 124 ASN A 128 TRP A 185 SITE 2 AC7 6 LYS A 186 HOH A2247 SITE 1 AC8 8 ARG A 60 GLU A 61 THR A 62 ASN A 65 SITE 2 AC8 8 HOH A2133 HOH A2135 HOH A2146 HOH A2294 SITE 1 AC9 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 1 BC1 6 ARG A 102 HIS A 103 ASN A 106 HOH A2201 SITE 2 BC1 6 HOH A2455 HOH A2456 SITE 1 BC2 6 TYR A 179 TYR A 181 ALA A 292 ILE A 293 SITE 2 BC2 6 ASN A 294 HOH A2454 SITE 1 BC3 2 GLN A 116 ASN A 117 SITE 1 BC4 3 ASP A 302 TYR A 303 MET A 306 CRYST1 71.410 71.410 150.590 90.00 90.00 90.00 P 43 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 0.014004 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014004 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006641 0.00000