HEADER GENE REGULATION 29-JAN-21 7ND1 TITLE FIRST-IN-CLASS SMALL MOLECULE INHIBITORS OF POLYCOMB REPRESSIVE TITLE 2 COMPLEX 1 (PRC1) RING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE RING2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HUNTINGTIN-INTERACTING PROTEIN 2-INTERACTING PROTEIN 3,HIP2- COMPND 5 INTERACTING PROTEIN 3,PROTEIN DING,RING FINGER PROTEIN 1B,RING1B,RING COMPND 6 FINGER PROTEIN 2,RING FINGER PROTEIN BAP-1,RING-TYPE E3 UBIQUITIN COMPND 7 TRANSFERASE RING2; COMPND 8 EC: 2.3.2.27; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: POLYCOMB COMPLEX PROTEIN BMI-1; COMPND 12 CHAIN: H; COMPND 13 SYNONYM: POLYCOMB GROUP RING FINGER PROTEIN 4,RING FINGER PROTEIN 51; COMPND 14 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: RNF2, BAP1, DING, HIPI3, RING1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: BMI1, PCGF4, RNF51; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POLYCOMB REPRESSIVE COMPLEX 1 (PRC1), INHIBITOR, GENE REGULATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.CIERPICKI,G.LUND,L.JAREMKO REVDAT 3 07-JUL-21 7ND1 1 JRNL REVDAT 2 23-JUN-21 7ND1 1 JRNL REVDAT 1 16-JUN-21 7ND1 0 JRNL AUTH S.SHUKLA,W.YING,F.GRAY,Y.YAO,M.L.SIMES,Q.ZHAO,H.MIAO, JRNL AUTH 2 H.J.CHO,P.GONZALEZ-ALONSO,A.WINKLER,G.LUND,T.PUROHIT,E.KIM, JRNL AUTH 3 X.ZHANG,J.M.RAY,S.HE,C.NIKOLAIDIS,J.NDOJ,J.WANG,L.JAREMKO, JRNL AUTH 4 M.JAREMKO,R.J.H.RYAN,M.L.GUZMAN,J.GREMBECKA,T.CIERPICKI JRNL TITL SMALL-MOLECULE INHIBITORS TARGETING POLYCOMB REPRESSIVE JRNL TITL 2 COMPLEX 1 RING DOMAIN. JRNL REF NAT.CHEM.BIOL. V. 17 784 2021 JRNL REFN ESSN 1552-4469 JRNL PMID 34155404 JRNL DOI 10.1038/S41589-021-00815-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK 2.4 REMARK 3 AUTHORS : BONVIN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ND1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292113661. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.3 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.12 MM [U-2H; U-13C; U-15N; CH3 REMARK 210 ILV] RING1B-BMI1, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N TROSY; 3D HNCA; 3D REMARK 210 HNCO; 3D HNCACO; 3D HN(CO)CA; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK, SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 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 APPLY THE FOLLOWING TO CHAINS: A, H 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 8 REMARK 465 PRO A 9 REMARK 465 THR A 10 REMARK 465 GLN A 11 REMARK 465 PRO A 12 REMARK 465 LEU A 13 REMARK 465 SER A 14 REMARK 465 LYS A 15 REMARK 465 SER A 116 REMARK 465 MET A 117 REMARK 465 HIS A 118 REMARK 465 ARG A 119 REMARK 465 SER H 1103 REMARK 465 ALA H 1104 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HZ3 LYS H 1051 O LYS H 1062 1.49 REMARK 500 OE2 GLU A 48 HZ2 LYS H 1081 1.54 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 1 TRP A 17 54.24 -110.44 REMARK 500 1 PRO A 52 5.66 -68.13 REMARK 500 1 ASP A 56 -168.53 -118.29 REMARK 500 1 ASN A 60 78.10 44.72 REMARK 500 1 CYS A 67 -1.77 -143.93 REMARK 500 1 SER A 96 -165.45 55.61 REMARK 500 1 ASP H1057 24.14 81.55 REMARK 500 1 THR H1063 -57.22 -127.69 REMARK 500 2 TRP A 17 54.12 -110.56 REMARK 500 2 PRO A 52 5.69 -68.02 REMARK 500 2 ASP A 56 -168.54 -118.30 REMARK 500 2 ASN A 60 78.01 44.65 REMARK 500 2 CYS A 67 -1.84 -143.89 REMARK 500 2 SER A 96 -167.81 58.84 REMARK 500 2 ASP H1057 24.26 81.31 REMARK 500 2 THR H1063 -57.29 -127.68 REMARK 500 3 TRP A 17 54.26 -110.57 REMARK 500 3 PRO A 52 5.65 -67.96 REMARK 500 3 ASP A 56 -168.55 -118.40 REMARK 500 3 ASN A 60 78.04 44.76 REMARK 500 3 CYS A 67 -1.72 -143.87 REMARK 500 3 SER A 96 -166.57 57.60 REMARK 500 3 ASP H1057 24.15 81.48 REMARK 500 3 THR H1063 -57.45 -127.68 REMARK 500 4 TRP A 17 54.17 -110.53 REMARK 500 4 PRO A 52 5.58 -67.96 REMARK 500 4 ASP A 56 -168.53 -118.32 REMARK 500 4 ASN A 60 78.01 44.80 REMARK 500 4 CYS A 67 -1.88 -143.90 REMARK 500 4 SER A 96 -166.37 58.96 REMARK 500 4 ASP H1057 24.13 81.51 REMARK 500 4 THR H1063 -57.38 -127.79 REMARK 500 5 TRP A 17 54.20 -110.56 REMARK 500 5 PRO A 52 5.69 -67.98 REMARK 500 5 ASP A 56 -168.54 -118.37 REMARK 500 5 ASN A 60 78.03 44.75 REMARK 500 5 CYS A 67 -1.81 -143.84 REMARK 500 5 SER A 96 -165.73 59.80 REMARK 500 5 ASP H1057 24.34 81.49 REMARK 500 5 THR H1063 -57.34 -127.73 REMARK 500 6 TRP A 17 54.25 -110.61 REMARK 500 6 PRO A 52 5.61 -67.98 REMARK 500 6 ASP A 56 -168.48 -118.41 REMARK 500 6 ASN A 60 78.02 44.73 REMARK 500 6 CYS A 67 -1.89 -143.83 REMARK 500 6 SER A 96 -170.67 61.54 REMARK 500 6 ASP H1057 24.11 81.52 REMARK 500 6 THR H1063 -57.37 -127.67 REMARK 500 7 TRP A 17 54.20 -110.60 REMARK 500 7 PRO A 52 5.53 -67.89 REMARK 500 REMARK 500 THIS ENTRY HAS 161 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL 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 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 51 SG REMARK 620 2 CYS A 54 SG 107.9 REMARK 620 3 CYS A 72 SG 110.6 113.6 REMARK 620 4 CYS A 75 SG 121.5 102.5 100.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 HIS A 69 ND1 105.0 REMARK 620 3 CYS A 87 SG 98.8 95.7 REMARK 620 4 CYS A 90 SG 119.4 110.9 123.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H1201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS H1018 SG REMARK 620 2 CYS H1039 SG 98.9 REMARK 620 3 CYS H1042 SG 90.4 103.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN H1202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS H1034 SG REMARK 620 2 HIS H1036 ND1 95.2 REMARK 620 3 CYS H1053 SG 123.7 118.1 REMARK 620 4 CYS H1056 SG 104.4 109.3 104.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34597 RELATED DB: BMRB REMARK 900 FIRST-IN-CLASS SMALL MOLECULE INHIBITORS OF POLYCOMB REPRESSIVE REMARK 900 COMPLEX 1 (PRC1) RING DOMAIN DBREF 7ND1 A 10 116 UNP Q99496 RING2_HUMAN 10 116 DBREF 7ND1 H 1004 1104 UNP P35226 BMI1_HUMAN 4 104 SEQADV 7ND1 GLY A 8 UNP Q99496 EXPRESSION TAG SEQADV 7ND1 PRO A 9 UNP Q99496 EXPRESSION TAG SEQADV 7ND1 MET A 117 UNP Q99496 EXPRESSION TAG SEQADV 7ND1 HIS A 118 UNP Q99496 EXPRESSION TAG SEQADV 7ND1 ARG A 119 UNP Q99496 EXPRESSION TAG SEQRES 1 A 112 GLY PRO THR GLN PRO LEU SER LYS THR TRP GLU LEU SER SEQRES 2 A 112 LEU TYR GLU LEU GLN ARG THR PRO GLN GLU ALA ILE THR SEQRES 3 A 112 ASP GLY LEU GLU ILE VAL VAL SER PRO ARG SER LEU HIS SEQRES 4 A 112 SER GLU LEU MET CYS PRO ILE CYS LEU ASP MET LEU LYS SEQRES 5 A 112 ASN THR MET THR THR LYS GLU CYS LEU HIS ARG PHE CYS SEQRES 6 A 112 ALA ASP CYS ILE ILE THR ALA LEU ARG SER GLY ASN LYS SEQRES 7 A 112 GLU CYS PRO THR CYS ARG LYS LYS LEU VAL SER LYS ARG SEQRES 8 A 112 SER LEU ARG PRO ASP PRO ASN PHE ASP ALA LEU ILE SER SEQRES 9 A 112 LYS ILE TYR PRO SER MET HIS ARG SEQRES 1 H 101 THR THR ARG ILE LYS ILE THR GLU LEU ASN PRO HIS LEU SEQRES 2 H 101 MET CYS VAL LEU CYS GLY GLY TYR PHE ILE ASP ALA THR SEQRES 3 H 101 THR ILE ILE GLU CYS LEU HIS SER PHE CYS LYS THR CYS SEQRES 4 H 101 ILE VAL ARG TYR LEU GLU THR SER LYS TYR CYS PRO ILE SEQRES 5 H 101 CYS ASP VAL GLN VAL HIS LYS THR ARG PRO LEU LEU ASN SEQRES 6 H 101 ILE ARG SER ASP LYS THR LEU GLN ASP ILE VAL TYR LYS SEQRES 7 H 101 LEU VAL PRO GLY LEU PHE LYS ASN GLU MET LYS ARG ARG SEQRES 8 H 101 ARG ASP PHE TYR ALA ALA HIS PRO SER ALA HET ZN A 201 1 HET ZN A 202 1 HET U9E A 203 42 HET ZN H1201 1 HET ZN H1202 1 HETNAM ZN ZINC ION HETNAM U9E 3-(2-CHLOROPHENYL)-4-ETHYL-5-(1~{H}-INDOL-4-YL)-1~{H}- HETNAM 2 U9E PYRROLE-2-CARBOXYLIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 U9E C21 H17 CL N2 O2 HELIX 1 AA1 SER A 20 ARG A 26 1 7 HELIX 2 AA2 LEU A 45 MET A 50 1 6 HELIX 3 AA3 ALA A 73 ARG A 81 1 9 HELIX 4 AA4 ASP A 103 SER A 111 1 9 HELIX 5 AA5 THR H 1010 MET H 1017 5 8 HELIX 6 AA6 LYS H 1040 GLU H 1048 1 9 HELIX 7 AA7 ARG H 1064 LEU H 1067 5 4 HELIX 8 AA8 ASP H 1072 VAL H 1083 1 12 HELIX 9 AA9 GLY H 1085 HIS H 1101 1 17 SHEET 1 AA1 2 GLU A 37 VAL A 40 0 SHEET 2 AA1 2 THR H1005 LYS H1008 -1 O THR H1005 N VAL A 40 SHEET 1 AA2 3 ARG A 70 CYS A 72 0 SHEET 2 AA2 3 THR A 61 THR A 64 -1 N MET A 62 O PHE A 71 SHEET 3 AA2 3 LEU A 100 PRO A 102 -1 O ARG A 101 N THR A 63 SHEET 1 AA3 3 HIS H1036 CYS H1039 0 SHEET 2 AA3 3 ALA H1028 ILE H1031 -1 N THR H1029 O PHE H1038 SHEET 3 AA3 3 ILE H1069 SER H1071 -1 O ARG H1070 N THR H1030 LINK SG CYS A 51 ZN ZN A 202 1555 1555 2.31 LINK SG CYS A 54 ZN ZN A 202 1555 1555 2.39 LINK SG CYS A 67 ZN ZN A 201 1555 1555 2.31 LINK ND1 HIS A 69 ZN ZN A 201 1555 1555 2.08 LINK SG CYS A 72 ZN ZN A 202 1555 1555 2.30 LINK SG CYS A 75 ZN ZN A 202 1555 1555 2.17 LINK SG CYS A 87 ZN ZN A 201 1555 1555 2.56 LINK SG CYS A 90 ZN ZN A 201 1555 1555 2.05 LINK SG CYS H1018 ZN ZN H1201 1555 1555 2.34 LINK SG CYS H1034 ZN ZN H1202 1555 1555 2.29 LINK ND1 HIS H1036 ZN ZN H1202 1555 1555 2.24 LINK SG CYS H1039 ZN ZN H1201 1555 1555 2.37 LINK SG CYS H1042 ZN ZN H1201 1555 1555 2.29 LINK SG CYS H1053 ZN ZN H1202 1555 1555 2.34 LINK SG CYS H1056 ZN ZN H1202 1555 1555 2.32 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 MODEL 1