satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)naphthalene-2-sulfonamide (PDB entry 5DYY)
Macromolecule: Cholinesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.8
Sequence length: 530 residues
Sequence: TEDDIIIATKNGKVRGMNLTVFGGTVTAFLGIPYAQPPLGRLRFKKPQSLTKWSDIWNATKYANSCCQNIDQSFPGFHGSEMWNPNTDLSEDCLYLNVWIPAPKPKNATVLIWIYGGGFQTGTSSLHVYDGKFLARVERVIVVSMNYRVGALGFLALPGNPEAPGNMGLFDQQLALQWVQKNIAAFGGNPKSVTLFGESAGAASVSLHLLSPGSHSLFTRAILQSGSFNAPWAVTSLYEARNRTLNLAKLTGCSRENETEIIKCLRNKDPQEILLNEAFVVPYGTPLSVNFGPTVDGDFLTDMPDILLELGQFKKTQILVGVNKDEGTAFLVYGAPGFSKDNNSIITRKEFQEGLKIFFPGVSEFGKESILFHYTDWVDDQRPENYREALGDVVGDYNFICPALEFTKKFSEWGNNAFFYYFEHRSSKLPWPEWMGVMHGYEIEFVFGLPLERRDNYTKAEEILSRSIVKRWANFAKYGNPNETQNNSTSWPVFKSTEQKYLTLNTESTRIMTKLRAQQCRFWTSFFPKV
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1866
R free: 0.2444
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM Sodium acetate 12% peg 4K
Matthews coefficient: 2.97
Solvent content (%): 58.55
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: 2017-01-18
HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 2F (PDB entry 7JIU)
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: 946 residues
Sequence: NREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.2118
R free: 0.2459
Average B factor: 46.35
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: NOT AVAILABLE
Matthews coefficient: 2.64
Solvent content (%): 53.36
Ligand: (3S)-3-benzyl-5-[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]-3-methyl-1,3-dihydro-2H-indol-2-one (VBS)
Ligand formula: C28 H25 N7 O
Ligand molecular weight: 475.544
Ligand SMILES: CCn1c2c(c(ncn2)c3ccc4c(c3)C(C(=O)N4)(C)Cc5ccccc5)nc1c6cnc(nc6)C
Ligand InChI: InChI=1S/C28H25N7O/c1-4-35-25(20-14-29-17(2)30-15-20)34-24-23(31-16-32-26(24)35)19-10-11-22-21(12-19)28(3,27(36)33-22)13-18-8-6-5-7-9-18/h5-12,14-16H,4,13H2,1-3H3,(H,33,36)/t28-/m0/s1
Release date: 2021-06-30
Crystal structure of PDE8A catalytic domain in complex with 3a (PDB entry 7CWG)
Macromolecule: High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 338 residues
Sequence: DDVPPRIARAMENEEYWDFDIFELEAATHNRPLIYLGLKMFARFGICEFLHCSESTLRSWLQIIEANYHSSNPYHNSTHSADVLHATAYFLSKERIKETLDPIDEVAALIAATIHDVDHPGRTNSFLCNAGSELAILYNDTAVLESHHAALAFQLTTGDDKCNIFKNMERNDYRTLRQGIIDMVLATEMTKHFEHVNKFVNSINKPLATLEENGETDKNQEVINTMLRTPENRTLIKRMLIKCADVSNPCRPLQYCIEWAARISEEYFSQTDEEKQQGLPVVMPVFDRNTCSIPKSQISFIDYFITDMFDAWDAFVDLPDLMQHLDNNFKYWKGLDEM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.27477
R free: 0.31747
Average B factor: 41.421
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 100mM Cacodylate Sodium pH 6.5, 15% Isopropanol, 30% Ethylene Glycol, 11% PEG3350
Matthews coefficient: 3.33
Solvent content (%): 62.01
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: 2021-09-01
Notum Riluzole (PDB entry 7BNJ)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.1641
R free: 0.1972
Average B factor: 31.2828
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.93
Solvent content (%): 36.15
Ligand: 6-(trifluoromethoxy)-1,3-benzothiazol-2-amine (657)
Ligand formula: C8 H5 F3 N2 O S
Ligand molecular weight: 234.198
Ligand SMILES: c1cc2c(cc1OC(F)(F)F)sc(n2)N
Ligand InChI: InChI=1S/C8H5F3N2OS/c9-8(10,11)14-4-1-2-5-6(3-4)15-7(12)13-5/h1-3H,(H2,12,13)
Release date: 2022-03-02
CRYSTAL STRUCTURE OF XIAP-BIR2 DOMAIN COMPLEXED WITH LIGAND BOUND (PDB entry 4WVU)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 98 residues
Sequence: MGSSHHHHHHSSGETVRFQGHMRNPAMYSEEARLKSFQNWPDYAHLTPRELASAGLYYTGIGDQVQCFACGGKLKNWEPGDRAWSEHRRHFPNCFFVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.1392
R free: 0.1781
Average B factor: 11.15
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: .98 M AMMONIUM SULFATE and .1 M AMMONIUM FORMATE.  Grew single crystals after streak seeding.
Matthews coefficient: 1.73
Solvent content (%): 28.97
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: 2015-03-04
FGFR1 kinase complex with inhibitor SN37115 (PDB entry 6C18)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GAMSGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.22269
R free: 0.26668
Average B factor: 44.145
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 20% MPEG 5000, 0.1 M sodium cacodylate pH 7.5, 0.2 M ammonium sulfate
Matthews coefficient: 2.3
Solvent content (%): 46.56
Ligand: 3-(2,6-dichloro-3,5-dimethoxyphenyl)-1-{(3S)-1-[(2E)-4-(dimethylamino)but-2-enoyl]pyrrolidin-3-yl}-7-[(propan-2-yl)amino]-3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one (YY5)
Ligand formula: C27 H35 Cl2 N7 O4
Ligand molecular weight: 592.517
Ligand SMILES: CC(C)Nc1ncc2c(n1)N(C(=O)N(C2)c3c(c(cc(c3Cl)OC)OC)Cl)C4CCN(C4)C(=O)C=CCN(C)C
Ligand InChI: InChI=1S/C27H35Cl2N7O4/c1-16(2)31-26-30-13-17-14-35(24-22(28)19(39-5)12-20(40-6)23(24)29)27(38)36(25(17)32-26)18-9-11-34(15-18)21(37)8-7-10-33(3)4/h7-8,12-13,16,18H,9-11,14-15H2,1-6H3,(H,30,31,32)/b8-7+/t18-/m0/s1
Release date: 2019-01-16
crystal structure of mitochondrial calcium uptake 2(MICU2) (PDB entry 6IIH)
Macromolecule: Endolysin,Calcium uptake protein 2, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 493 residues
Sequence: MGHHHHHHMNIFEMLRIDERLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSIWYNQTPNRAKRVITTFRTGTWDAYHMLRKQRFMQFSSLEHEGEYYMTPRDFLFSVMFEQMERKTSVKKLTKKDIEDTLSGIQTAGCGSTFFRDLGDKGLISYTEYLFLLTILTKPHSGFHVAFKMLDTDGNEMIEKREFFKLQKIISKQDDLMTVKTNETGYQEAIVKEPEINTTLQMRFFGKRGQRKLHYKEFRRFMENLQTEIQEMEFLQFSKGLSFMRKEDFAEWLLFFTNTENKDIYWKNVREKLSAGESISLDEFKSFCHFTTHLEDFAIAMQMFSLAHRPVRLAEFKRAVKVATGQELSNNILDTVFKIFDLDGDECLSHEEFLGVLKNRMHRGLWVPQHQS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.958
R work: 0.1796
R free: 0.2274
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.16
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Sodium phosphate monobasic , 100 mM potassium phosphate monobasic , 100 mM MES, 6.0 and 1M sodium chloride
Matthews coefficient: 2.39
Solvent content (%): 48.59
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: 2019-08-14
Crystal structure of JAK2 JH1 in complex with cerdulatinib (PDB entry 8BX6)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 316 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1735
R free: 0.202
Average B factor: 28.25
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M Gly-Gly pH 8.2, 1.6 M Na-malonate
Matthews coefficient: 2.49
Solvent content (%): 50.51
Ligand: Cerdulatinib (S5I)
Ligand formula: C20 H27 N7 O3 S
Ligand molecular weight: 445.538
Ligand SMILES: CCS(=O)(=O)N1CCN(CC1)c2ccc(cc2)Nc3ncc(c(n3)NC4CC4)C(=O)N
Ligand InChI: InChI=1S/C20H27N7O3S/c1-2-31(29,30)27-11-9-26(10-12-27)16-7-5-15(6-8-16)24-20-22-13-17(18(21)28)19(25-20)23-14-3-4-14/h5-8,13-14H,2-4,9-12H2,1H3,(H2,21,28)(H2,22,23,24,25)
Release date: 2023-12-20
Crystal structure of hMTH1 N33A in complex with LW14 in the presence of acetate (PDB entry 6GLL)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWAGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.395
R work: 0.1836
R free: 0.1991
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5, 20% DMSO, 10 mM compound
Ligand: 1~{H}-imidazo[4,5-b]pyridin-2-amine (BU8)
Ligand formula: C6 H6 N4
Ligand molecular weight: 134.139
Ligand SMILES: c1cc2c(nc1)nc([nH]2)N
Ligand InChI: InChI=1S/C6H6N4/c7-6-9-4-2-1-3-8-5(4)10-6/h1-3H,(H3,7,8,9,10)
Release date: 2019-02-20
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM010032a (PDB entry 5RAH)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.1803
R free: 0.2052
Average B factor: 31.447
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.78
Solvent content (%): 55.69
Ligand: cyclopropyl-[4-(4-fluorophenyl)piperazin-1-yl]methanone (GX4)
Ligand formula: C14 H17 F N2 O
Ligand molecular weight: 248.296
Ligand SMILES: c1cc(ccc1N2CCN(CC2)C(=O)C3CC3)F
Ligand InChI: InChI=1S/C14H17FN2O/c15-12-3-5-13(6-4-12)16-7-9-17(10-8-16)14(18)11-1-2-11/h3-6,11H,1-2,7-10H2
Release date: 2020-04-22
DNA Polymerase Lambda, TTP:At Mg2+ Reaction State Ternary Complex, 120 sec (PDB entry 7M45)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 329 residues
Sequence: AQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.889
R work: 0.2045
R free: 0.2421
Average B factor: 42.3298
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Matthews coefficient: 2.83
Solvent content (%): 56.47
Ligand: THYMIDINE-5'-TRIPHOSPHATE (TTP)
Ligand formula: C10 H17 N2 O14 P3
Ligand molecular weight: 482.168
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Release date: 2022-07-06
Crystal Structure of Shp2 E76K GOF Mutant in the Open Conformation (PDB entry 6CRF)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: GMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAKLVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.198
R free: 0.237
Average B factor: 71.95
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M MES pH 6.5, 12% PEG 20,000, and 5% Sucrose
Matthews coefficient: 2.69
Solvent content (%): 54.28
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: 2018-11-07
Crystal structure of human O-GlcNAc transferase bound to a peptide from HCF-1 pro-repeat 2 (11-26) and inhibitor 2a (PDB entry 6MA3)
Macromolecule: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.255
Sequence length: 723 residues
Sequence: GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIKPVE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1858
R free: 0.2117
Average B factor: 35.7646
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 1.05 M Sodium Citrate Tribasic Dihydrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Matthews coefficient: 3.08
Solvent content (%): 60.01
Ligand: 4-{2-[(1R)-2-{(carboxymethyl)[(thiophen-2-yl)methyl]amino}-2-oxo-1-{[(2-oxo-1,2-dihydroquinolin-6-yl)sulfonyl]amino}ethyl]phenoxy}butanoic acid (JAJ)
Ligand formula: C28 H27 N3 O9 S2
Ligand molecular weight: 613.659
Ligand SMILES: c1ccc(c(c1)C(C(=O)N(Cc2cccs2)CC(=O)O)NS(=O)(=O)c3ccc4c(c3)C=CC(=O)N4)OCCCC(=O)O
Ligand InChI: InChI=1S/C28H27N3O9S2/c32-24-12-9-18-15-20(10-11-22(18)29-24)42(38,39)30-27(21-6-1-2-7-23(21)40-13-3-8-25(33)34)28(37)31(17-26(35)36)16-19-5-4-14-41-19/h1-2,4-7,9-12,14-15,27,30H,3,8,13,16-17H2,(H,29,32)(H,33,34)(H,35,36)/t27-/m1/s1
Release date: 2018-10-17
Crystal structure of PIM1 in complex with ARC-1411 (PDB entry 7OOV)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: SMLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1616
R free: 0.1947
Average B factor: 46.597
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 22% PEG3350, 0.1 M ammonium sulfate, 0.1 M tris pH 8.5
Matthews coefficient: 2.89
Solvent content (%): 57.46
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: 2021-08-04
Protein Tyrosine Phosphatase 1B N193A mutant in complex with TCS401, closed state (PDB entry 5KAD)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 306 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLAFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1759
R free: 0.2049
Average B factor: 22.5984
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris, pH 8.0, 0.2 M MgCl2, 17.5% PEG8000
Matthews coefficient: 2.26
Solvent content (%): 45.63
Ligand: 2-(OXALYL-AMINO)-4,5,6,7-TETRAHYDRO-THIENO[2,3-C]PYRIDINE-3-CARBOXYLIC ACID (OTA)
Ligand formula: C10 H10 N2 O5 S
Ligand molecular weight: 270.262
Ligand SMILES: C1CNCc2c1c(c(s2)NC(=O)C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C10H10N2O5S/c13-7(10(16)17)12-8-6(9(14)15)4-1-2-11-3-5(4)18-8/h11H,1-3H2,(H,12,13)(H,14,15)(H,16,17)
Release date: 2017-03-01
Crystal structure of the CSF1R kinase domain with a dihydropurinone inhibitor (compound 4) (PDB entry 6T2W)
Macromolecule: Macrophage colony-stimulating factor 1 receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 332 residues
Sequence: QKPKYQVRWKIIESYEGNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKEDAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGPVLVITEYCCYGDLLNFLRRKAEAMLGPSLSPGQDPEGLDKEDGRPLELRDLLHFSSQVAQGMAFLASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVKGNARLPVKWMAPESIFDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPKNIYSIMQACWALEPTHRPTFQQICSFLQEQAQEDRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.166
R free: 0.187
Average B factor: 28.09
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 16% PEG3350, 0.15 M Ammonium Sulfate, 0.1 M PCTP pH 5.5
Matthews coefficient: 2.47
Solvent content (%): 50.24
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: 2020-01-01
Peptide VACKSSQP in complex with human cathepsin V C25A mutant (PDB entry 7QFF)
Macromolecule: Cathepsin L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.43
Sequence length: 221 residues
Sequence: LPKSVDWRKKGYVTPVKNQKQCGSAWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVAQDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSQNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
Oligomeric state: Hetero 5-mer
Stoichiometry: A2, B2, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1691
R free: 0.1944
Average B factor: 29.87
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 77 % MPD, 23 % of 60 mM TRIS, pH 8
Matthews coefficient: 2.82
Solvent content (%): 56.36
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2022-12-21