satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of RBR ubiquitin ligase ARIH2 (PDB entry 7OD1)
Macromolecule: E3 ubiquitin-protein ligase ARIH2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.31
Sequence length: 493 residues
Sequence: MSVDMNSQGSDSNEEDYDPNCEEEEEEEEDDPGDIEDYYVGVASDVEQQGADAFDPEEYQFTCLTYKESEGALNEHMTSLASVLKVSHSVAKLILVNFHWQVSEILDRYKSNSAQLLVEARVQPNPSKHVPTSHPPHHCAVCMQFVRKENLLSLACQHQFCRSCWEQHCSVLVKDGVGVGVSCMAQDCPLRTPEDFVFPLLPNEELREKYRRYLFRDYVESHYQLQLCPGADCPMVIRVQEPRARRVQCNRCNEVFCFKCRQMYHAPTDCATIRKWLTKCADDSETANYISAHTKDCPKCNICIEKNGGCNHMQCSKCKHDFCWMCLGDWKTHGSEYYECSRYKENPDIVNQSQQAQAREALKKYLFYFERWENHNKSLQLEAQTYQRIHEKIQERVMNNLGTWIDWQYLQNAAKLLAKCRYTLQYTYPYAYYMESGPRKKLFEYQQAQLEAEIENLSWKVERADSYDRGDLENQMHIAEQRRRTLLKDFHDT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2203
R free: 0.2617
Average B factor: 76.8698
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Sodium nitrate, 0.1 M Bis-Tris propane pH 8.5, 20 % PEG 3350
Matthews coefficient: 2.39
Solvent content (%): 48.56
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: 2021-09-15
Structure of protein kinase CK2 catalytic subunit with the CK2beta-competitive bisubstrate inhibitor ARC3140 (PDB entry 6SPW)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 391 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ
Oligomeric state: Hetero 4-mer
Stoichiometry: A3, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.599
R work: 0.1645
R free: 0.196
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 1 MIKROLITER OF THE CK2ALPHA/ARC3140
MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR ARC3140, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 2.5 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 30 % PEG4000, 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, PH 5.6) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST MICROLITER OF THE RESERVOIR SOLUTION.
Matthews coefficient: 2.02
Solvent content (%): 39.21
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-01-29
Human PARP16 in complex with RBN010860 (PDB entry 6W65)
Macromolecule: Protein mono-ADP-ribosyltransferase PARP16
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2
Sequence length: 277 residues
Sequence: SMGWAAAREAAGRDMLAADLRCSLFASALQSYKRDSVLRPFPASYARGDCKDFEALLADASKLPNLKELLQSSGDNHKRAWDLVSWILSSKVLTIHSAGKAEFEKIQKLTGAPHTPVPAPDFLFEIEYFDPANAKFYETKGERDLIYAFHGSRLENFHSIIHNGLHCHLNKTSLFGEGTYLTSDLSLALIYSPHGHGWQHSLLGPILSCVAVCEVIDHPDVKCQTKKKDSKEIDRRRARIKHSEGGDIPPKYFVVTNNQLLRVKYLLVYSQKPPKRA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.1901
R free: 0.2247
Average B factor: 55.531
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 100mM Sodium citrate pH5.5, 18%w/v PEG3350
Matthews coefficient: 2.88
Solvent content (%): 57.33
Ligand: 5-{5-[(piperidin-4-yl)oxy]-2H-isoindol-2-yl}-4-(trifluoromethyl)pyridazin-3(2H)-one (T9D)
Ligand formula: C18 H17 F3 N4 O2
Ligand molecular weight: 378.348
Ligand SMILES: c1cc2cn(cc2cc1OC3CCNCC3)C4=C(C(=O)NN=C4)C(F)(F)F
Ligand InChI: InChI=1S/C18H17F3N4O2/c19-18(20,21)16-15(8-23-24-17(16)26)25-9-11-1-2-14(7-12(11)10-25)27-13-3-5-22-6-4-13/h1-2,7-10,13,22H,3-6H2,(H,24,26)
Release date: 2020-10-07
LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-chlorophenyl)(3-(piperidin-1-yl)propoxy)methyl)-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (Compound N48) (PDB entry 6BH5)
Macromolecule: Lysine-specific demethylase 5A, linked KDM5A JMJ domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.651
R work: 0.1952
R free: 0.216
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2), 0-20% glycerol, 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.21
Solvent content (%): 44.41
Ligand: 2-{(S)-(2-chlorophenyl)[3-(piperidin-1-yl)propoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid (DNY)
Ligand formula: C23 H26 Cl N3 O3
Ligand molecular weight: 427.924
Ligand SMILES: c1ccc(c(c1)C(c2cc3c([nH]2)c(ccn3)C(=O)O)OCCCN4CCCCC4)Cl
Ligand InChI: InChI=1S/C23H26ClN3O3/c24-18-8-3-2-7-16(18)22(30-14-6-13-27-11-4-1-5-12-27)20-15-19-21(26-20)17(23(28)29)9-10-25-19/h2-3,7-10,15,22,26H,1,4-6,11-14H2,(H,28,29)/t22-/m0/s1
Release date: 2018-03-28
Phosphorylated ERK2 in complex with ORF45 (PDB entry 7OPM)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 364 residues
Sequence: GSASMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2352
R free: 0.2535
Average B factor: 77.717
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris pH 8.3, 20% PEG 8000 with 1.25 M NaCl in reservoir
Matthews coefficient: 2.44
Solvent content (%): 49.57
Ligand: 1-[4-(hydroxymethyl)-1H-pyrazolo[4,3-c]pyridin-6-yl]-3-[(1S)-1-phenylethyl]urea (08G)
Ligand formula: C16 H17 N5 O2
Ligand molecular weight: 311.338
Ligand SMILES: CC(c1ccccc1)NC(=O)Nc2cc3c(cn[nH]3)c(n2)CO
Ligand InChI: InChI=1S/C16H17N5O2/c1-10(11-5-3-2-4-6-11)18-16(23)20-15-7-13-12(8-17-21-13)14(9-22)19-15/h2-8,10,22H,9H2,1H3,(H,17,21)(H2,18,19,20,23)/t10-/m0/s1
Release date: 2022-02-02
HCoV-229E RBD Class V in complex with human APN (PDB entry 6U7G)
Macromolecule: Aminopeptidase N
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.2
Sequence length: 906 residues
Sequence: GGRPDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVIIIHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSEFEGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPKDLTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRIWARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTYRENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLGADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGASVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMNRWTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWLIDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQIINDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNYLKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWMENPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWILNRYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNLIQAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWFTENSK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1786
R free: 0.2184
Average B factor: 43.2781
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 9% PEG8000, 1 mM oxidized glutathione, 1 mM reduced glutathione, 5% glycerol, 100 mM MES, pH 6.5
Matthews coefficient: 2.96
Solvent content (%): 58.41
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: 2019-11-13
Human DNA Ligase 1 Bound to an Adenylated, dideoxy Terminated DNA nick with 2 mM Mg2+ (PDB entry 6P0A)
Macromolecule: DNA ligase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.5.1.1
Sequence length: 645 residues
Sequence: SNDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1699
R free: 0.2033
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, 100 mM Lithium Acetate, 15 % (w/v) PEG 3350
Matthews coefficient: 2.43
Solvent content (%): 49.45
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2019-12-11
Human GAR transformylase in complex with GAR and (S)-2-(7-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanamido)pentanedioic acid (AGF145) (PDB entry 4ZYZ)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.2.2
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1646
R free: 0.1876
Average B factor: 21.3294
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 18 % PEG4000, 2 % PEG400, 0.33 M NaCl
Matthews coefficient: 3.89
Solvent content (%): 68.35
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2016-04-20
Human AlkB homolog ALKBH6 in complex with Tris and Ni (PDB entry 7VJS)
Macromolecule: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 246 residues
Sequence: MEEQDARVPALEPFRVEQAPPVIYYVPDFISKEEEEYLLRQVFNAPKPKWTQLSGRKLQNWGGLPHPRGMVPERLPPWLQRYVDKVSNLSLFGGLPANHVLVNQYLPGEGIMPHEDGPLYYPTVSTISLGSHTVLDFYEPRRPEDDDPTEQPRPPPRPTTSLLLEPRSLLVLRGPAYTRLLHGIAAARVDALDAASSPPNAAACPSARPGACLVRGTRVSLTIRRVPRVLRAGLLLGKGTENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.792
R work: 0.1969
R free: 0.2144
Average B factor: 22.654
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 8000, Tris
Matthews coefficient: 2.64
Solvent content (%): 53.48
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2022-02-02
Ternary complex crystal structure of DNA polymerase Beta with A:A mismatch at the primer terminus (PDB entry 5J29)
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: 0.2115
R free: 0.2829
Average B factor: 27.7056
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: 2.3
Solvent content (%): 46.52
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
Structure of TcdA GTD in complex with RhoA (PDB entry 7U2P)
Macromolecule: Glucosyltransferase TcdA
Type: Protein, polypeptide(L)
Source organism: Clostridioides difficile
EC number: 2.4.1
Sequence length: 543 residues
Sequence: SMSLISKEELIKLAYSIRPRENEYKTILTNLDEYNKLTTNNNENKYLQLKKLNESIDVFMNKYKTSSRNRALSNLKKDILKEVILIKNSNTSPVEKNLHFVWIGGEVSDIALEYIKQWADINAEYNIKLWYDSEAFLVNTLKKAIVESSTTEALQLLEEEIQNPQFDNMKFYKKRMEFIYDRQKRFINYYASQINKPTVPTIDDIIKSHLVSEYNRDETVLESYRTNSLRKINSNHGIDIRANSLFTEQELLNIYSQELLNRGNLAAASDIVRLLALKNFGGVYLDVDMLPGIHSDLFKTISRPSSIGLDRWEMIKLEAIMKYKKYINNYTSENFDKLDQQLKDNFKLIIESKSEKSEIFSKLENLNVSDLEIKIAFALGSVINQALISKQGSYLTNLVIEQVKNRYQFLNQHLNPAIESDNNFTDTTKIFHDSLFNSATAENSMFLTKIAPYLQVGFMPEARSTISLSGPGAYASAYYDFINLQENTIEKTLKASDLIEFKFPENNLSQLTEQEINSLWSFDQASAKYQFEKYVRDYTGGSL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.596
R work: 0.2149
R free: 0.2354
Average B factor: 60.029
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Ammonium sulfate, 0.1 M MES, pH 5.9, and 10% (w/v) PEG 8000
Matthews coefficient: 2.68
Solvent content (%): 54.04
Ligand: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPG)
Ligand formula: C15 H24 N2 O17 P2
Ligand molecular weight: 566.302
Ligand SMILES: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
Ligand InChI: InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1
Release date: 2022-05-04
Human dihydroorotase mutant F1563T co-crystallized with carbamoyl aspartate at pH 7.5 (PDB entry 6HFQ)
Macromolecule: CAD protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.5.5
Sequence length: 393 residues
Sequence: GPMTSQKLVRLPGLIDVHVHLREPGGTHKEDFASGTAAALAGGITMVCAMPNTRPPIIDGPALALAQKLAEAGARCDFALFLGASSENAGTLGTVAGSAAGLKLYLNETTSELRLDSVVQWMEHFETWPSHLPIVAHAEQQTVAAVLMVAQLTQRSVHICHVARKEEILLIKAAKARGLPVTCEVAPHHLFLSHDDLERLGPGKGEVRPELGSRQDVEALWENMAVIDCFASDHAPHTLEEKCGSRPPPGFPGLETMLPLLLTAVSEGRLSLDDLLQRLHHNPRRIFHLPPQEDTYVEVDLEHEWTIPSHMPFSKAHWTPFEGQKVKGTVRRVVLRGEVAYIDGQVLVPPGYGQDVRKWPQGAVPQLPPSAPATSEMTTTPERPRRGIPGLPD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.14542458871
R work: 0.124958636067
R free: 0.137050568255
Average B factor: 20.7193285176
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: Protein at 2-3 mg/ml in 20 mM Tris pH 8, 0.15 M NaCl, 0.02 mM zinc sulfate, 0.2 mM TCEP with 4 mM carbamoyl asparate.
Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.52
Solvent content (%): 51.11
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: 2018-10-24
Crystal structure of c-Cbl TKBD domain in complex with SPRY2 peptide (36-60, pY55) Refined to 1.8A Resolution (P6 form) (PDB entry 5HKY)
Macromolecule: E3 ubiquitin-protein ligase CBL
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 308 residues
Sequence: SNAPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1569
R free: 0.1801
Average B factor: 27.744
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% (v/v) PEG 400, 0.1M HEPES, 200 mM MgCl2
Matthews coefficient: 3.29
Solvent content (%): 62.59
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-01-18
Glycogen Synthase Kinase 3 beta Complexed with BRD0209 (PDB entry 5KPK)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 424 residues
Sequence: GSPGMSGRPRTTSFAESCKPVQQPSAFGSMKVSRDKDGSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQAAASTPTNATAASDANTGDRGQTNNAASASASNST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.167
R free: 0.2236
Average B factor: 55.822
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: Reservoir: 0.15 M DL-malic acid, pH 7.0, 20% w/v PEG3350
Matthews coefficient: 2.98
Solvent content (%): 58.78
Ligand: (4~{S})-3-cyclopropyl-4,7,7-trimethyl-4-phenyl-2,6,8,9-tetrahydropyrazolo[3,4-b]quinolin-5-one (6VK)
Ligand formula: C22 H25 N3 O
Ligand molecular weight: 347.453
Ligand SMILES: CC1(CC2=C(C(=O)C1)C(c3c([nH]nc3N2)C4CC4)(C)c5ccccc5)C
Ligand InChI: InChI=1S/C22H25N3O/c1-21(2)11-15-17(16(26)12-21)22(3,14-7-5-4-6-8-14)18-19(13-9-10-13)24-25-20(18)23-15/h4-8,13H,9-12H2,1-3H3,(H2,23,24,25)/t22-/m1/s1
Release date: 2018-03-14
Thrombin in complex with (S)-1-((R)-2-amino-3-cyclohexylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide (PDB entry 5JZY)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 259 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.27
R work: 0.1202
R free: 0.1423
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Sodium dihydrogen phosphate ph 7.5, 
350 mM NaCl, 
27% PEG 8000
Matthews coefficient: 2.5
Solvent content (%): 50.2
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: 2017-06-07
Rapid development of two Factor IXa inhibitors from Hit to Lead (PDB entry 4YZU)
Macromolecule: Coagulation factor IX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.22
Sequence length: 235 residues
Sequence: VVGGEDAKPGQFPWQVVLNGKVDAFCGGSIVNEKWIVTAAHCVETGVKITVVAGEHNIEETEHTEQKRNVIRIIPHHNYNAAINKYNHDIALLELDEPLVLNSYVTPICIADKEYTNIFLKFGSGYVSGWGRVFHKGASALVLQYLRVPLVDRATCLRSTKFTIYNNMFCAGFHEGGRDSCQGDSGGPHVTEVEGTSFLTGIISWGEECAMKGKYGIYTKVSRYVNWIKEKTKLT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.145
R free: 0.161
Average B factor: 26.65
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.05 M Tris, pH 7.2, 1.2 M ammonium sulfate, 2.0 M sodium chloride
Matthews coefficient: 2.75
Solvent content (%): 55.31
Ligand: N-[2-(5,6-dimethyl-1H-benzimidazol-2-yl)ethyl]-4-(4H-1,2,4-triazol-4-yl)benzamide (4K6)
Ligand formula: C20 H20 N6 O
Ligand molecular weight: 360.412
Ligand SMILES: Cc1cc2c(cc1C)nc([nH]2)CCNC(=O)c3ccc(cc3)n4cnnc4
Ligand InChI: InChI=1S/C20H20N6O/c1-13-9-17-18(10-14(13)2)25-19(24-17)7-8-21-20(27)15-3-5-16(6-4-15)26-11-22-23-12-26/h3-6,9-12H,7-8H2,1-2H3,(H,21,27)(H,24,25)
Release date: 2015-05-20
Factor VIIa in complex with the inhibitor (11R)-11-[(1-aminoisoquinolin-6-yl)amino]-16-(cyclopropylsulfonyl)-13-methyl-2,13-diazatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaene-3,12-dione (PDB entry 5TQF)
Macromolecule: Factor VIIa (Heavy Chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 254 residues
Sequence: IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1833
R free: 0.2085
Average B factor: 28.19
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000
Matthews coefficient: 3.88
Solvent content (%): 68.28
Ligand: (11R)-11-[(1-aminoisoquinolin-6-yl)amino]-16-(cyclopropylsulfonyl)-13-methyl-2,13-diazatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaene-3,12-dione (7KR)
Ligand formula: C31 H31 N5 O4 S
Ligand molecular weight: 569.674
Ligand SMILES: CN1Cc2cc(ccc2S(=O)(=O)C3CC3)NC(=O)CCc4cccc(c4)C(C1=O)Nc5ccc6c(c5)ccnc6N
Ligand InChI: InChI=1S/C31H31N5O4S/c1-36-18-22-17-23(7-11-27(22)41(39,40)25-8-9-25)34-28(37)12-5-19-3-2-4-21(15-19)29(31(36)38)35-24-6-10-26-20(16-24)13-14-33-30(26)32/h2-4,6-7,10-11,13-17,25,29,35H,5,8-9,12,18H2,1H3,(H2,32,33)(H,34,37)/t29-/m1/s1
Release date: 2017-02-01