satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure the peptide-substrate-binding domain of human type II collagen prolyl 4-hydroxylase complexed with Pro-Pro-Gly-Pro-Glu-Gly-Pro-Pro-Gly. (PDB entry 6EVP)
Macromolecule: Prolyl 4-hydroxylase subunit alpha-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.2
Sequence length: 102 residues
Sequence: MHHHHHHMLSVDDCFGMGRSAYNEGDYYHTVLWMEQVLKQLDAGEEATTTKSQVLDYLSYAVFQLGDLHRALELTRRLLSLDPSHERAGGNLRYFEQLLEEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.68
R work: 0.1827
R free: 0.2151
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 2.45 M ammonium sulphate, 10% DMSO, 100 mM MOPS, 5 mM PPGPEGPPG, 5% PEG 400, 100 mM MOPS.
Matthews coefficient: 2.69
Solvent content (%): 54.31
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2018-09-12
The Crystal Structure of human DHFR from Biortus (PDB entry 7ESE)
Macromolecule: Dihydrofolate reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.3
Sequence length: 204 residues
Sequence: MGGSHHHHHHENLYFQGMVGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.2405
R free: 0.285
Average B factor: 32.357
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.15M KBr, 30% PEGMME 2000
Matthews coefficient: 1.9
Solvent content (%): 35.17
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2021-05-26
Ternary complex crystal structure of DNA polymerase Beta with T:G mismatch at the primer terminus (PDB entry 5J2J)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2008
R free: 0.2659
Average B factor: 26.0554
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.31
Solvent content (%): 46.69
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2016-10-26
Human Xylosyltransferase 1 in complex with peptide QEEEGSAGGQGG (PDB entry 6EJB)
Macromolecule: Xylosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.26
Sequence length: 751 residues
Sequence: APLVHHHHHHALDENLYFQGALADVSRPPHARKTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRFCPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHVDKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFINLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGDRRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSPHCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKFEAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGLRRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVMPKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTVTVIWVDPVNVIAATYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVAPLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGTALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.557
R work: 0.2393
R free: 0.2795
Average B factor: 44.3944
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 55-65% Morpheus Precipitant mix 2 (PEG8000 and Ethylene glycol)
0.1M Bicine/Tris buffer at pH 7.5
0.1M of NPS mix (0.033M of each)
Matthews coefficient: 2.56
Solvent content (%): 51.94
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2018-05-02
Nek2 bound to arylaminopurine 6 (PDB entry 5M57)
Macromolecule: Serine/threonine-protein kinase Nek2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 279 residues
Sequence: MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKAFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2186
R free: 0.2742
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3 % PEG 8000, 50 mM Tris pH 8.5
Matthews coefficient: 2.41
Solvent content (%): 49
Ligand: O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE (4SP)
Ligand formula: C18 H22 N6 O3 S
Ligand molecular weight: 402.471
Ligand SMILES: c1cc(ccc1Nc2nc3c(c(n2)OCC4CCCCC4)nc[nH]3)S(=O)(=O)N
Ligand InChI: InChI=1S/C18H22N6O3S/c19-28(25,26)14-8-6-13(7-9-14)22-18-23-16-15(20-11-21-16)17(24-18)27-10-12-4-2-1-3-5-12/h6-9,11-12H,1-5,10H2,(H2,19,25,26)(H2,20,21,22,23,24)
Release date: 2016-11-23
Gcase in complex with small molecule inhibitor 1 (PDB entry 9FAY)
Macromolecule: Lysosomal acid glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 546 residues
Sequence: MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.14812
R free: 0.1831
Average B factor: 23.787
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M KSCN
25% PEG 3350
Matthews coefficient: 2.15
Solvent content (%): 42.73
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2024-07-03
Crystal structure of SND1 in complex with C-26-A2 (PDB entry 7KNW)
Macromolecule: Staphylococcal nuclease domain-containing protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.31.1
Sequence length: 324 residues
Sequence: MGSSHHHHHHSSGENLYFQGVPTVQRGIIKMVLSGCAIIVRGQPRGGPPPERQINLSNIRAGNLARRAAKDTPDEPWAFPAREFLRKKLIGKEVCFTIENKTPQGREYGMIYLGKDTNGENIAESLVAEGLATRREGMRANNPEQNRLSECEEQAKAAKKGMWSEGNGSHTIRDLKYTIENPRHFVDSHHQKPVNAIIEHVRDGSVVRALLLPDYYLVTVMLSGIKCPTFRRETPEPFAAEAKFFTESRLLQRDVQIILESCHNQNILGTILHPNGNITELLLKEGFARCVDWSIAVYTRGAEKLRAAERFAKERRLRIWRDYV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2635
R free: 0.3376
Average B factor: 50.281
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M MES-NaOH pH 6.2, 1.0 M trisodium citrate
Matthews coefficient: 2.56
Solvent content (%): 51.87
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2021-12-08
The Human NatA (Naa10/Naa15) amino-terminal acetyltransferase complex (PDB entry 6C9M)
Macromolecule: N-alpha-acetyltransferase 15, NatA auxiliary subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 866 residues
Sequence: MPAVSLPPKENALFKRILRCYEHKQYRNGLKFCKQILSNPKFAEHGETLAMKGLTLNCLGKKEEAYELVRRGLRNDLKSHVCWHVYGLLQRSDKKYDEAIKCYRNALKWDKDNLQILRDLSLLQIQMRDLEGYRETRYQLLQLRPAQRASWIGYAIAYHLLEDYEMAAKILEEFRKTQQTSPDKVDYEYSELLLYQNQVLREAGLYREALEHLCTYEKQICDKLAVEETKGELLLQLCRLEDAADVYRGLQERNPENWAYYKGLEKALKPANMLERLKIYEEAWTKYPRGLVPRRLPLNFLSGEKFKECLDKFLRMNFSKGCPPVFNTLRSLYKDKEKVAIIEELVVGYETSLKSCRLFNPNDDGKEEPPTTLLWVQYYLAQHYDKIGQPSIALEYINTAIESTPTLIELFLVKAKIYKHAGNIKEAARWMDEAQALDTADRFINSKCAKYMLKANLIKEAEEMCSKFTREGTSAVENLNEMQCMWFQTECAQAYKAMNKFGEALKKCHEIERHFIEITDDQFDFHTYCMRKITLRSYVDLLKLEDVLRQHPFYFKAARIAIEIYLKLHDNPLTDENKEHEADTANMSDKELKKLRNKQRRAQKKAQIEEEKKNAEKEKQQRNQKKKKDDDDEEIGGPKEELIPEKLAKVETPLEEAIKFLTPLKNLVKNKIETHLFAFEIYFRKEKFLLMLQSVKRAFAIDSSHPWLHECMIRLFNTAVCESKDLSDTVRTVLKQEMNRLFGATNPKNFNETFLKRNSDSLPHRLSAAKMVYYLDPSSQKRAIELATTLDESLTNRNLQTCMEVLEALYDGSLGDCKEAAEIYRANCHKLFPYALAFMPPGYEEDMKITVNGDSSAEAEELANEI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.187
R free: 0.242
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG3350, 10% Tascimate, pH 7.5, 2% acetone
Matthews coefficient: 2.85
Solvent content (%): 56.89
Ligand: INOSITOL HEXAKISPHOSPHATE (IHP)
Ligand formula: C6 H18 O24 P6
Ligand molecular weight: 660.035
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
Release date: 2018-06-06
Crystal structure of the human RAD9-RAD1(F64A/M256A/F266A)-HUS1-RHINO(88-99) complex (PDB entry 8WU8)
Macromolecule: Cell cycle checkpoint control protein RAD9A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.11.2
Sequence length: 270 residues
Sequence: MKCLVTGGNVKVLGKAVHSLSRIGDELYLEPLEDGLSLRTVNSSRSAYACFLFAPLFFQQYQAATPGQDLLRCKILMKSFLSVFRSLAMLEKTVEKCCISLNGRSSRLVVQLHCKFGVRKTHNLSFQDCESLQAVFDPASCPHMLRAPARVLGEAVLPFSPALAEVTLGIGRGRRVILRSYHEEEADSTAKAMVTEMCLGEEDFQQLQAQEGVAITFCLKEFRGLLSFAESANLNLSIHFDAPGRPAIFTIKDSLLDGHFVLATLSDTDS
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.81
R work: 0.2148
R free: 0.2669
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, Potassium iodine
Matthews coefficient: 2.17
Solvent content (%): 43.36
Release date: 2024-02-14
CRYSTAL STRUCTURE OF BRAF(V600E) IN COMPLEX WITH LY3009120 COMPND (PDB entry 5C9C)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 307 residues
Sequence: MDRGSHHHHHHGSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATEKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPKIHR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.194
R free: 0.238
Average B factor: 24.92
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 26% PEG 3350, 50 MM AMMONIUM
 CITRATE, 50 MM SODIUM FLORIDE, 2 MG/ML PROTEIN, 5-FOLD MOLAR
 EXCESS DP4978; CRYSTAL ID 215552F10, SITTING DROP VAPOR
 DIFFUSION, TEMPERATURE 289K
Matthews coefficient: 2.59
Solvent content (%): 52.5
Ligand: 1-(3,3-dimethylbutyl)-3-{2-fluoro-4-methyl-5-[7-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-6-yl]phenyl}urea (4Z5)
Ligand formula: C23 H29 F N6 O
Ligand molecular weight: 424.514
Ligand SMILES: Cc1cc(c(cc1c2cc3cnc(nc3nc2C)NC)NC(=O)NCCC(C)(C)C)F
Ligand InChI: InChI=1S/C23H29FN6O/c1-13-9-18(24)19(29-22(31)26-8-7-23(3,4)5)11-16(13)17-10-15-12-27-21(25-6)30-20(15)28-14(17)2/h9-12H,7-8H2,1-6H3,(H2,26,29,31)(H,25,27,28,30)
Release date: 2015-07-15
Crystal Structure of human phosphodiesterase 10 in complex with 6-methyl-3-(2-phenylpyrazol-3-yl)-1-[3-(trifluoromethoxy)phenyl]pyridazin-4-one (PDB entry 5SK4)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1844
R free: 0.2237
Average B factor: 39.579
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.64
Solvent content (%): 53.35
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-10-12
Crystal structure of TDP1 complexed with compound XZ768 (PDB entry 7UFZ)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.559
R work: 0.1708
R free: 0.1948
Average B factor: 28.8442
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MOPS/HEPES-Na pH 7.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.03 M sodium fluoride, 0.03 M sodium bromide and 0.03 M sodium iodide
Matthews coefficient: 2.42
Solvent content (%): 49.1
Ligand: (4-{[(4S)-2-phenylimidazo[1,2-a]pyridin-3-yl]amino}phenyl)phosphonic acid (N7U)
Ligand formula: C19 H16 N3 O3 P
Ligand molecular weight: 365.322
Ligand SMILES: c1ccc(cc1)c2c(n3ccccc3n2)Nc4ccc(cc4)P(=O)(O)O
Ligand InChI: InChI=1S/C19H16N3O3P/c23-26(24,25)16-11-9-15(10-12-16)20-19-18(14-6-2-1-3-7-14)21-17-8-4-5-13-22(17)19/h1-13,20H,(H2,23,24,25)
Release date: 2023-04-12
Crystal structure of IRE1a in complex with compound 18 (PDB entry 6URC)
Macromolecule: Serine/threonine-protein kinase/endoribonuclease IRE1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 434 residues
Sequence: GSSPSLEQDDGDEETSVVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLQQTTSGLAHLHSLNIVHRDLKPHNILISMPNAHGKIKAMISDFGLCKKLAVGRHSFSRRSGVPGTEGWIAPEMLSEDCKENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQANILLGACSLDCLHPEKHEDVIARELIEKMIAMDPQKRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYFTSRFPHLLAHTYRAMELCSHERLFQPYYFHEPPEPQPPVTPDALGNS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2202
R free: 0.274
Average B factor: 26.4432
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M trisodium citrate pH 5.6, 10% isopropanol, 10% PEG4000, and cesium chloride
Matthews coefficient: 2.52
Solvent content (%): 51.1
Ligand: 2-chloro-N-(6-methyl-5-{[3-(2-{[(3S)-piperidin-3-yl]amino}pyrimidin-4-yl)pyridin-2-yl]oxy}naphthalen-1-yl)benzene-1-sulfonamide (QFV)
Ligand formula: C31 H29 Cl N6 O3 S
Ligand molecular weight: 601.118
Ligand SMILES: Cc1ccc2c(c1Oc3c(cccn3)c4ccnc(n4)NC5CCCNC5)cccc2NS(=O)(=O)c6ccccc6Cl
Ligand InChI: InChI=1S/C31H29ClN6O3S/c1-20-13-14-22-23(8-4-11-27(22)38-42(39,40)28-12-3-2-10-25(28)32)29(20)41-30-24(9-6-17-34-30)26-15-18-35-31(37-26)36-21-7-5-16-33-19-21/h2-4,6,8-15,17-18,21,33,38H,5,7,16,19H2,1H3,(H,35,36,37)/t21-/m0/s1
Release date: 2019-11-06
HER3 pseudokinase domain bound to bosutinib (PDB entry 6OP9)
Macromolecule: Receptor tyrosine-protein kinase erbB-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 328 residues
Sequence: KRAMRRYLERGESIEPLDPSEKANKVLARIFKETELRKLKVLGSGVFGTVHKGVWIPEGESIKIPVCIKVIEDKSGRQSFQAVTDHMLAIGSLDHAHIVRLLGLCPGSSLQLVTQYLPLGSLLDHVRQHRGALGPQLLLNWGVQIAKGMYYLEEHGMVHRNLAARNVLLKSPSQVQVADFGVADLLPPDDKQLLYSEAKTPIKWMALESIHFGKYTHQSDVWSYGVTVWELMTFGAEPYAGLRLAEVPDLLEKGERLAQPQICTIDVYMVMVKCWMIDENIRPTFKELANEFTRMARDPPRYLVIKRESGPGIAPGPEPHGLTNKKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.501
R work: 0.1704
R free: 0.2302
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 20000, 0.1M MES, pH 6.7
Matthews coefficient: 3.08
Solvent content (%): 60.06
Ligand: 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile (DB8)
Ligand formula: C26 H29 Cl2 N5 O3
Ligand molecular weight: 530.446
Ligand SMILES: CN1CCN(CC1)CCCOc2cc3c(cc2OC)c(c(cn3)C#N)Nc4cc(c(cc4Cl)Cl)OC
Ligand InChI: InChI=1S/C26H29Cl2N5O3/c1-32-6-8-33(9-7-32)5-4-10-36-25-13-21-18(11-24(25)35-3)26(17(15-29)16-30-21)31-22-14-23(34-2)20(28)12-19(22)27/h11-14,16H,4-10H2,1-3H3,(H,30,31)
Release date: 2019-08-21
Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D (PDB entry 5E8F)
Macromolecule: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 149 residues
Sequence: SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1983
R free: 0.2561
Average B factor: 34.13
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES (pH 7.5), 0.2 M Li2SO4, 25 % PEG4000 and 0.1 M NaOAc
Matthews coefficient: 2.61
Solvent content (%): 52.89
Ligand: GERAN-8-YL GERAN (GER)
Ligand formula: C20 H34
Ligand molecular weight: 274.484
Ligand SMILES: CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
Ligand InChI: InChI=1S/C20H34/c1-7-18(4)12-9-14-20(6)16-10-15-19(5)13-8-11-17(2)3/h7,11,14-15H,8-10,12-13,16H2,1-6H3/b18-7+,19-15+,20-14+
Release date: 2015-11-18
Crystal structure of a human Cdc34-ubiquitin thioester mimetic (PDB entry 6NYO)
Macromolecule: Ubiquitin-conjugating enzyme E2 R2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 204 residues
Sequence: GAMAQQQMTSSQKALMLELKSLQEEPVEGFRITLVDESDLYNWEVAIFGPPNTLYEGGYFKAHIKFPIDYPYSPPTFRFLTKMWHPNIYENGDVKISILHPPVDDPQSGELPSERWNPTQNVRTILLSVISLLNEPNTFSPANVDASVMFRKWRDSKGKDKEYAEIIRKQVSATKAEAEKDGVKVPTTLAEYCIKTKVPSNDNS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.502
R work: 0.1748
R free: 0.2022
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.03 M potassium dihydrogen phosphate, 23% PEG 8,000
Matthews coefficient: 2.33
Solvent content (%): 47.17
Ligand: 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid (U94)
Ligand formula: C20 H21 Cl2 N O6
Ligand molecular weight: 442.29
Ligand SMILES: COCC(=O)NC(Cc1ccc(cc1)c2cc(cc(c2)Cl)Cl)C(C(C(=O)O)O)O
Ligand InChI: InChI=1S/C20H21Cl2NO6/c1-29-10-17(24)23-16(18(25)19(26)20(27)28)6-11-2-4-12(5-3-11)13-7-14(21)9-15(22)8-13/h2-5,7-9,16,18-19,25-26H,6,10H2,1H3,(H,23,24)(H,27,28)/t16-,18-,19+/m0/s1
Release date: 2019-08-07
Crystal structure of the human METTL3-METTL14 complex with compound UOZ059a (PDB entry 7NIA)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1938
R free: 0.2351
Average B factor: 45.51
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.12
Solvent content (%): 41.86
Ligand: 4-[[(3R)-3-cyclopropyl-2-azaspiro[3.3]heptan-2-yl]methyl]-N-[[(3R)-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide (UEQ)
Ligand formula: C34 H42 N6 O2
Ligand molecular weight: 566.736
Ligand SMILES: c1ccc(cc1)CNc2cc(ncn2)N3CCCC(C3)(CNC(=O)c4ccc(cc4)CN5CC6(C5C7CC7)CCC6)O
Ligand InChI: InChI=1S/C34H42N6O2/c41-32(28-10-8-26(9-11-28)20-40-22-33(14-4-15-33)31(40)27-12-13-27)36-21-34(42)16-5-17-39(23-34)30-18-29(37-24-38-30)35-19-25-6-2-1-3-7-25/h1-3,6-11,18,24,27,31,42H,4-5,12-17,19-23H2,(H,36,41)(H,35,37,38)/t31-,34-/m1/s1
Release date: 2021-10-20