satarupa22/MacromolecularLigandDB huggingface dataset:
HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) having oxidized catalytic cysteine and complexed with 6-(difluoromethyl)pyrimidin-4-ol at two allosteric sites (PDB entry 8TK3)
Macromolecule: Dual specificity protein phosphatase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 183 residues
Sequence: GSFELSVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.18617
R free: 0.25538
Average B factor: 31.256
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: The protein in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA was mixed with the crystallization buffer (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the crystallization buffer. The crystals were soaked with 25 mM of the compound in solution (10% DMSO, 100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000).
Matthews coefficient: 2.21
Solvent content (%): 44.46
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2024-08-14
Crystal structure of TrkA in complex with PF-00593174 (PDB entry 5JFS)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 308 residues
Sequence: MHHHHHHLVPRGSVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.1699
R free: 0.1909
Average B factor: 31.97
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C
Matthews coefficient: 3
Solvent content (%): 62.95
Ligand: N-{4-[4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-2-yl}-N'-(2,4-difluorophenyl)urea (6K0)
Ligand formula: C22 H19 F2 N7 O2
Ligand molecular weight: 451.429
Ligand SMILES: CC(C)n1cc(c2c1ncnc2N)C(=O)c3ccnc(c3)NC(=O)Nc4ccc(cc4F)F
Ligand InChI: InChI=1S/C22H19F2N7O2/c1-11(2)31-9-14(18-20(25)27-10-28-21(18)31)19(32)12-5-6-26-17(7-12)30-22(33)29-16-4-3-13(23)8-15(16)24/h3-11H,1-2H3,(H2,25,27,28)(H2,26,29,30,33)
Release date: 2017-03-01
Kinase domain of ALK2-K493A with AMPPNP (PDB entry 6UNQ)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 330 residues
Sequence: MSYYHHHHHHHHHHDYDIPTTENLYFQGAMGQRTVARQITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKATLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2178
R free: 0.2826
Average B factor: 71.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES 6.5 pH, 20 %v/v Ethylene glycol, 7 %w/v PEG 8000
Matthews coefficient: 2.34
Solvent content (%): 47.39
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2021-07-07
Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese, product ligand and UDP (Product complex III) (PDB entry 4WN2)
Macromolecule: Xyloside xylosyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.4.2
Sequence length: 306 residues
Sequence: SLEGGVVVPVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEASREVAKALLRELLPPAAGFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAGSGTYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPELFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIPED
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.19485
R free: 0.23853
Average B factor: 36.386
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Li2SO4, 0.1 M Bis-Tris, and 21% PEG3350
Matthews coefficient: 2.43
Solvent content (%): 49.35
Ligand: URIDINE-5'-DIPHOSPHATE (UDP)
Ligand formula: C9 H14 N2 O12 P2
Ligand molecular weight: 404.161
Ligand SMILES: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
Release date: 2015-09-30
DNA Polymerase Mu, dGTP:Ct Pre-Catalytic Ground State Ternary Complex, 10 mM Ca2+ (20min) (PDB entry 7KSS)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.503
R work: 0.1599
R free: 0.1769
Average B factor: 26.204
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.52
Solvent content (%): 51.19
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2022-05-11
The crystal structure of human DNMT1(351-1600) (PDB entry 4WXX)
Macromolecule: DNA (cytosine-5)-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 1256 residues
Sequence: SPKCIQCGQYLDDPDLKYGQHPPDAVDEPQMLTNEKLSIFDANESGFESYEALPQHKLTCFSVYCKHGHLCPIDTGLIEKNIELFFSGSAKPIYDDDPSLEGGVNGKNLGPINEWWITGFDGGEKALIGFSTSFAEYILMDPSPEYAPIFGLMQEKIYISKIVVEFLQSNSDSTYEDLINKIETTVPPSGLNLNRFTEDSLLRHAQFVVEQVESYDEAGDSDEQPIFLTPCMRDLIKLAGVTLGQRRAQARRQTIRHSTREKDRGPTKATTTKLVYQIFDTFFAEQIEKDDREDKENAFKRRRCGVCEVCQQPECGKCKACKDMVKFGGSGRSKQACQERRCPNMAMKEADDDEEVDDNIPEMPSPKKMHQGKKKKQNKNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAMEGGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKALTRVW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.622
R work: 0.2049
R free: 0.2453
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 289
Crystal growth procedure: 45% PEG200, 50 mM CaCl2, 0.1 mM MES
Matthews coefficient: 3.74
Solvent content (%): 67.13
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: 2015-07-15
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with PCM-0102245-001 (PDB entry 7G9H)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.746
R work: 0.2015
R free: 0.2737
Average B factor: 66.87
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.45
Solvent content (%): 49.89
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-07-12
EGFR kinase domain with compound 41a (PDB entry 5CAV)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.73
R work: 0.197
R free: 0.2313
Average B factor: 77.73
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 292
Crystal growth procedure: sodium/potassium tartrate
Matthews coefficient: 3.47
Solvent content (%): 64.51
Ligand: (1R)-1-{6-({2-[(3R,4S)-3-fluoro-4-methoxypiperidin-1-yl]pyrimidin-4-yl}amino)-1-[(2S)-1,1,1-trifluoropropan-2-yl]-1H-imidazo[4,5-c]pyridin-2-yl}ethanol (4ZQ)
Ligand formula: C21 H25 F4 N7 O2
Ligand molecular weight: 483.463
Ligand SMILES: CC(c1nc2cnc(cc2n1C(C)C(F)(F)F)Nc3ccnc(n3)N4CCC(C(C4)F)OC)O
Ligand InChI: InChI=1S/C21H25F4N7O2/c1-11(33)19-28-14-9-27-18(8-15(14)32(19)12(2)21(23,24)25)29-17-4-6-26-20(30-17)31-7-5-16(34-3)13(22)10-31/h4,6,8-9,11-13,16,33H,5,7,10H2,1-3H3,(H,26,27,29,30)/t11-,12+,13-,16+/m1/s1
Release date: 2015-10-28
PI3K alpha in complex with an inhibitor (PDB entry 7TZ7)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 1074 residues
Sequence: MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSKKLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIFHTIKQHALNHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.2389
R free: 0.2773
Average B factor: 90.6423
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 303.15
Crystal growth procedure: 0.15M Potassium Thiocyanate, 20% PEG 3350
Matthews coefficient: 2.31
Solvent content (%): 46.85
Ligand: (4S,5R)-3-[2'-amino-2-(morpholin-4-yl)-4'-(trifluoromethyl)[4,5'-bipyrimidin]-6-yl]-4-(hydroxymethyl)-5-methyl-1,3-oxazolidin-2-one (KVJ)
Ligand formula: C18 H20 F3 N7 O4
Ligand molecular weight: 455.391
Ligand SMILES: CC1C(N(C(=O)O1)c2cc(nc(n2)N3CCOCC3)c4cnc(nc4C(F)(F)F)N)CO
Ligand InChI: InChI=1S/C18H20F3N7O4/c1-9-12(8-29)28(17(30)32-9)13-6-11(24-16(25-13)27-2-4-31-5-3-27)10-7-23-15(22)26-14(10)18(19,20)21/h6-7,9,12,29H,2-5,8H2,1H3,(H2,22,23,26)/t9-,12+/m1/s1
Release date: 2022-05-18
Human EphA3 Kinase domain in complex with Birb796 (PDB entry 4TWN)
Macromolecule: Ephrin type-A receptor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 361 residues
Sequence: MGSSHHHHHHSSGLVPRGSTQTVHEFAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLSRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAARPSNLLLDQSNVDITTFRTTGDWLNGVWTAHCKEIFTGVEYSSCDTIAKIS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.706
R work: 0.1769
R free: 0.2127
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium cacodylate pH 6.5, 0.15M ammonium sulfate, 22.5% PEG 3350
Matthews coefficient: 1.91
Solvent content (%): 35.73
Ligand: 1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA (B96)
Ligand formula: C31 H37 N5 O3
Ligand molecular weight: 527.657
Ligand SMILES: Cc1ccc(cc1)n2c(cc(n2)C(C)(C)C)NC(=O)Nc3ccc(c4c3cccc4)OCCN5CCOCC5
Ligand InChI: InChI=1S/C31H37N5O3/c1-22-9-11-23(12-10-22)36-29(21-28(34-36)31(2,3)4)33-30(37)32-26-13-14-27(25-8-6-5-7-24(25)26)39-20-17-35-15-18-38-19-16-35/h5-14,21H,15-20H2,1-4H3,(H2,32,33,37)
Release date: 2015-05-13
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-2-methyl-N-(2-morpholin-4-yl-[1,2,4]triazolo[1,5-c]pyrimidin-7-yl)pyrazole-3-carboxamide (PDB entry 5SGC)
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): 2.09
R work: 0.181
R free: 0.235
Average B factor: 43.885
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: 2.63
Solvent content (%): 53.26
Ligand: 4-(azetidine-1-carbonyl)-1-methyl-N-[(4S)-2-(morpholin-4-yl)[1,2,4]triazolo[1,5-c]pyrimidin-7-yl]-1H-pyrazole-5-carboxamide (IWK)
Ligand formula: C18 H21 N9 O3
Ligand molecular weight: 411.418
Ligand SMILES: Cn1c(c(cn1)C(=O)N2CCC2)C(=O)Nc3cc4nc(nn4cn3)N5CCOCC5
Ligand InChI: InChI=1S/C18H21N9O3/c1-24-15(12(10-20-24)17(29)25-3-2-4-25)16(28)21-13-9-14-22-18(23-27(14)11-19-13)26-5-7-30-8-6-26/h9-11H,2-8H2,1H3,(H,21,28)
Release date: 2022-10-12
Pre-catalytic ternary complex of human Polymerase Mu (G433S) mutant with incoming nonhydrolyzable UMPNPP (PDB entry 5VZA)
Macromolecule: DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 9 residues
Sequence: CGGCATACG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.501
R work: 0.1688
R free: 0.1838
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 90mM HEPES pH 7.5, 18% PEG4K
Matthews coefficient: 2.52
Solvent content (%): 51.18
Ligand: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine (2KH)
Ligand formula: C9 H16 N3 O14 P3
Ligand molecular weight: 483.156
Ligand SMILES: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O14P3/c13-5-1-2-12(9(16)10-5)8-7(15)6(14)4(25-8)3-24-27(17,18)11-28(19,20)26-29(21,22)23/h1-2,4,6-8,14-15H,3H2,(H,10,13,16)(H2,21,22,23)(H3,11,17,18,19,20)/t4-,6-,7-,8-/m1/s1
Release date: 2017-07-05
Crystal structure of the PI3KC2alpha C2 domain in space group C121 (PDB entry 6BTZ)
Macromolecule: Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.154
Sequence length: 131 residues
Sequence: SNAIGGAVKLSISYRNGTLFIMVMHIKDLVTEDGADPNPYVKTYLLPDNHKTSKRKTKISRKTRNPTFNEMLVYSGYSKETLRQRELQLSVLSAESLRENFFLGGVTLPLKDFNLSKETVKWYQLTAATYL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1866
R free: 0.2148
Average B factor: 21.61
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: PEG 400, (NH4)2SO4
Matthews coefficient: 2.45
Solvent content (%): 49.82
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: 2018-10-17
Human CDK8-CYCC in complex with compound 4: N-methyl-4-(4-pyridyl)-1H-pyrrole-2-carboxamide (PDB entry 5XQX)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 380 residues
Sequence: GAMGSHMEFMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1878
R free: 0.22186
Average B factor: 36.317
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.05M MgCl, 0.1M MES pH 6.5, 10% Iso-propanol, 5% PEG4K
Matthews coefficient: 3.06
Solvent content (%): 59.81
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: 2017-08-09
Fibroblast growth factor receptor 1 kinase in complex with JK-P5 (PDB entry 4UWB)
Macromolecule: FIBROBLAST GROWTH FACTOR RECEPTOR 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: GAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.22892
R free: 0.27172
Average B factor: 54.516
Crystal growth procedure: 20% PEG8000, 20% ETHLYENE GLYCOL, 0.2M AMMONIUM SULPHATE, 0.1M PCTP PH 6.75
Matthews coefficient: 2.7
Solvent content (%): 54
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2015-09-02
Crystal structure of Dot1L in complex with an inhibitor (compound 11). (PDB entry 6TEN)
Macromolecule: Histone-lysine N-methyltransferase, H3 lysine-79 specific
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 334 residues
Sequence: GPGEKLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYEPFSPEVYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.179
R free: 0.201
Average B factor: 63.46
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 1.5 M Li sulfate
0.1 M Hepes pH 7.0
Matthews coefficient: 3.53
Solvent content (%): 65.11
Ligand: 3-[(4-azanyl-6-methoxy-1,3,5-triazin-2-yl)amino]-4-[[(~{S})-[2,2-bis(fluoranyl)-1,3-benzodioxol-4-yl]-(3-chloranylpyridin-2-yl)methyl]amino]benzenesulfonamide (N5K)
Ligand formula: C23 H19 Cl F2 N8 O5 S
Ligand molecular weight: 592.962
Ligand SMILES: COc1nc(nc(n1)Nc2cc(ccc2NC(c3cccc4c3OC(O4)(F)F)c5c(cccn5)Cl)S(=O)(=O)N)N
Ligand InChI: InChI=1S/C23H19ClF2N8O5S/c1-37-22-33-20(27)32-21(34-22)31-15-10-11(40(28,35)36)7-8-14(15)30-17(18-13(24)5-3-9-29-18)12-4-2-6-16-19(12)39-23(25,26)38-16/h2-10,17,30H,1H3,(H2,28,35,36)(H3,27,31,32,33,34)/t17-/m0/s1
Release date: 2019-12-11