satarupa22/MacromolecularLigandDB huggingface dataset:
XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010954a (PDB entry 5S88)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1595
R free: 0.1787
Average B factor: 18.553
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Matthews coefficient: 2.6
Solvent content (%): 52.69
Ligand: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine (LU8)
Ligand formula: C27 H32 N2 O3
Ligand molecular weight: 432.555
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H32N2O3/c1-18-23(21-8-6-19(7-9-21)20-10-12-29(2)13-11-20)16-28-17-24(18)22-14-25(30-3)27(32-5)26(15-22)31-4/h6-9,14-17,20H,10-13H2,1-5H3
Release date: 2021-06-23
CLK3 A319V mutant bound with benzothiazole Tg003 (Cpd 2) (PDB entry 6YTY)
Macromolecule: Dual specificity protein kinase CLK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 360 residues
Sequence: SMQSSKRSSRSVEDDKEGHLVCRIGDWLQERYEIVGNLGEGTFGKVVECLDHARGKSQVALKIIRNVGKYREAARLEINVLKKIKEKDKENKFLCVLMSDWFNFHGHMCIAFELLGKNTFEFLKENNFQPYPLPHVRHMAYQLCHALRFLHENQLTHTDLKPENILFVNSEFETLYNEHKSCEEKSVKNTSIRVVDFGSATFDHEHHTTIVATRHYRPPEVILELGWAQPCDVWSIGCILFEYYRGFTLFQTHENREHLVMMEKILGPIPSHMIHRTRKQKYFYKGGLVWDENSSDGRYVKENCKPLKSYMLQDSLEHVQLFDLMRRMLEFDPAQRITLAEALLHPFFAGLTPEERSFHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.1864
R free: 0.2235
Average B factor: 15.915
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG 3350, 0,2M NaBr, 10% Ethylene Glycol, 0.1M bis-tris propane
Matthews coefficient: 2.21
Solvent content (%): 44.24
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: 2020-07-15
Human DNA polymerase eta-DNA ternary complex: reaction with 1 mM Mn2+ for 1800s (PDB entry 5KFF)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1825
R free: 0.2208
Average B factor: 22.6442
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.1
Solvent content (%): 41.31
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2016-06-22
Co-crystal structure of Human Nicotinamide N-methyltransferase (NNMT) with the bisubstrate-like inhibitor (33) (PDB entry 7NBM)
Macromolecule: Nicotinamide N-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.1
Sequence length: 283 residues
Sequence: MGSSHHHHHHSSGLVPRGSMESGFTSKDTYLSHFNPRDYLEKYYKFGSRHSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKAAPAAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSSLPLGREAVEAAVKEAGYTIEWFEVISQSYSSTMANNEGLFSLVARKLSRPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.691
R work: 0.2088
R free: 0.3144
Average B factor: 48
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Human NNMT was crystallized using the following conditions: A protein solution with 6 mg/ml NNMT, 50 mM Tris/HCL, pH 8.0, 1 mM DTT, 0.95mM inhibitor and 5% v/v glycerol was equilibrated at room temperature in a hanging drop setup against 2.2 M ammonium sulfate with 0.1 M HEPES/Na, pH 7.6. Small crystal appeared after 1-2 weeks.
Matthews coefficient: 2.21
Solvent content (%): 44.4
Ligand: (E)-3-((5,6-dihydro-2H,4H-thiazolo[5,4,3-ij]quinolin-2-ylidene)amino)-2-hydroxy-1-(4-(isoquinolin-5-yl)piperazin-1-yl)-2-methylpropan-1-one (U7K)
Ligand formula: C27 H29 N5 O2 S
Ligand molecular weight: 487.616
Ligand SMILES: CC(CN=C1N2CCCc3c2c(ccc3)S1)(C(=O)N4CCN(CC4)c5cccc6c5ccnc6)O
Ligand InChI: InChI=1S/C27H29N5O2S/c1-27(34,18-29-26-32-12-4-7-19-5-3-9-23(35-26)24(19)32)25(33)31-15-13-30(14-16-31)22-8-2-6-20-17-28-11-10-21(20)22/h2-3,5-6,8-11,17,34H,4,7,12-16,18H2,1H3/b29-26+/t27-/m0/s1
Release date: 2021-03-17
Crystal structure of the complex of 059-152-Fv and EGFR-ECD (PDB entry 5XWD)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 651 residues
Sequence: MRPSGTAGAALLALLAALCPASRALEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQEVAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEILHGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGEENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTCPPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVRKCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHTPPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLNITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENSCKATGQVCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCNLLEGEPREFVENSECIQCHPECLPQAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNCTYGCTGPGLEGCPTNGPKIGSENLYFQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.894
R work: 0.2768
R free: 0.3309
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: MES buffer (pH 6.0), zinc acetate, PEG8000
Matthews coefficient: 3.54
Solvent content (%): 65.23
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: 2018-02-28
Crystal structure of human SHIP2 Phosphatase-C2 D607A mutant (PDB entry 5OKN)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 461 residues
Sequence: GPEPDMISVFIGTWNMGSVPPPKNVTSWFTSKGLGKTLDEVTVTIPHDIYVFGTQENSVGDREWLDLLRGGLKELTDLDYRPIAMQSLWNIKVAVLVKPEHENRISHVSTSSVKTGIANTLGNKGAVGVSFMFNGTSFGFVNCHLTSGNEKTARRNQNYLDILRLLSLGDRQLNAFDISLRFTHLFWFGALNYRLDMDIQEILNYISRKEFEPLLRVDQLNLEREKHKVFLRFSEEEISFPPTYRYERGSRDTYAWHKQKPTGVRTNVPSWCDRILWKSYPETHIICNSYGCTDDIVTSDHSPVFGTFEVGVTSQFISKKGLSKTSDQAYIEFESIEAIVKTASRTKFFIEFYSTCLEEYKKSFENDAQSSDNINFLKVQWSSRQLPTLKPILADIEYLQDQHLLLTVKSMDGYESYGECVVALKSMIGSTAQQFLTFLSHRGEETGNIRGSMKVRVPTER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.206
R free: 0.24463
Average B factor: 60.007
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Bis-Tris propane, pH 7.0, 0.4 M KSCN, 20% (w/v) PEG3350
Matthews coefficient: 2.59
Solvent content (%): 52.5
Ligand: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (B3P)
Ligand formula: C11 H26 N2 O6
Ligand molecular weight: 282.334
Ligand SMILES: C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
Ligand InChI: InChI=1S/C11H26N2O6/c14-4-10(5-15,6-16)12-2-1-3-13-11(7-17,8-18)9-19/h12-19H,1-9H2
Release date: 2017-08-23
Crystal Structure of the N-terminal domain of human METTL16 in complex with SAH (PDB entry 6B92)
Macromolecule: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 294 residues
Sequence: SNAMALSKSMHARNRYKDKPPDFAYLASKYPDFKQHVQINLNGRVSLNFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNPRRPPPSSVNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFYD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.181
R free: 0.219
Average B factor: 54.009
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M K2HPO4, 45 mM NaH2PO4; drop contained 4 uL of protein solution (27 mg/mL) and 2 uL of reservoir solution; 0.2 uL of 200 mM SAM solution (buffered in 50 mM Hepes pH7.5) was added to the drop with mature crystals. 25% ethylene glycol was used for cryo-protection
Matthews coefficient: 4.77
Solvent content (%): 74.23
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: 2018-04-04
Crystal structure of Cdk2 in complex with Cyclin A inhibitor 6-[(E)-2-(4-chlorophenyl)ethenyl]-2-{[(2R)-3-(4-hydroxyphenyl)-1-methoxy-1-oxopropan-2-yl]carbamoyl}quinoline-4-carboxylic acid (PDB entry 8CUR)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1975
R free: 0.2674
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 0.2 M sodium chloride, 0.1 M MES, pH 6.0, 20% PEG6000
Matthews coefficient: 2.02
Solvent content (%): 39.15
Ligand: 6-[(E)-2-(4-chlorophenyl)ethenyl]-2-{[(2R)-3-(4-hydroxyphenyl)-1-methoxy-1-oxopropan-2-yl]carbamoyl}quinoline-4-carboxylic acid (OW6)
Ligand formula: C29 H23 Cl N2 O6
Ligand molecular weight: 530.956
Ligand SMILES: COC(=O)C(Cc1ccc(cc1)O)NC(=O)c2cc(c3cc(ccc3n2)C=Cc4ccc(cc4)Cl)C(=O)O
Ligand InChI: InChI=1S/C29H23ClN2O6/c1-38-29(37)26(15-19-6-11-21(33)12-7-19)32-27(34)25-16-23(28(35)36)22-14-18(8-13-24(22)31-25)3-2-17-4-9-20(30)10-5-17/h2-14,16,26,33H,15H2,1H3,(H,32,34)(H,35,36)/b3-2+/t26-/m1/s1
Release date: 2023-04-05
Crystal structure of V561M FGFR1 gatekeeper mutation (C488A, C584S, V561M) in complex with N-{3-[2-(3,5-DIMETHOXYPHENYL)ETHYL]-1H-PYRAZOL-5-YL}-4-[(3R,5S)-3,5-DIMETHYLPIPERAZIN-1-YL]BENZAMIDE (AZD4547) (PDB entry 4RWK)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 317 residues
Sequence: MGHHHHHHMAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIMEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.982
R work: 0.2376
R free: 0.2986
Average B factor: 32.804
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.6, 34% PEG 8000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 2.29
Solvent content (%): 46.21
Ligand: N-{3-[2-(3,5-dimethoxyphenyl)ethyl]-1H-pyrazol-5-yl}-4-[(3R,5S)-3,5-dimethylpiperazin-1-yl]benzamide (66T)
Ligand formula: C26 H33 N5 O3
Ligand molecular weight: 463.572
Ligand SMILES: CC1CN(CC(N1)C)c2ccc(cc2)C(=O)Nc3cc(n[nH]3)CCc4cc(cc(c4)OC)OC
Ligand InChI: InChI=1S/C26H33N5O3/c1-17-15-31(16-18(2)27-17)22-9-6-20(7-10-22)26(32)28-25-13-21(29-30-25)8-5-19-11-23(33-3)14-24(12-19)34-4/h6-7,9-14,17-18,27H,5,8,15-16H2,1-4H3,(H2,28,29,30,32)/t17-,18+
Release date: 2015-04-15
Pre-catalytic ternary complex of human Polymerase Mu (G433A) mutant with incoming nonhydrolyzable UMPNPP (PDB entry 5VZ7)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 354 residues
Sequence: GSAAASPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLAWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.551
R work: 0.1701
R free: 0.188
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 50mM HEPES pH 7.5, 10% PEG4K
Matthews coefficient: 2.51
Solvent content (%): 51.01
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 human carbonic anhydrase II in complex with the inhibitor 4-(phenethylthio)benzenesulfonamide (PDB entry 6GOT)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1988
R free: 0.2233
Average B factor: 15.776
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, Tris 100 mM
Matthews coefficient: 2.09
Solvent content (%): 41.18
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: 2018-10-03
Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK (PDB entry 5TO3)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 46 residues
Sequence: SEYQTFFNPRTFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.34
R work: 0.214
R free: 0.255
Average B factor: 47.7
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM HEPES and 20% PEG 8000
Matthews coefficient: 3
Solvent content (%): 60
Ligand: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide (0G6)
Ligand formula: C21 H34 Cl N6 O3
Ligand molecular weight: 453.986
Ligand SMILES: c1ccc(cc1)CC(C(=O)N2CCCC2C(=O)NC(CCCNC(=[NH2+])N)C(CCl)O)N
Ligand InChI: InChI=1S/C21H33ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-18,29H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/p+1/t15-,16+,17+,18-/m1/s1
Release date: 2017-03-29
Thrombin in complex with benzamidine (PDB entry 4UEH)
Macromolecule: HIRUDIN VARIANT-2
Type: Protein, polypeptide(L)
Source organism: Hirudo medicinalis
Sequence length: 12 residues
Sequence: GDFEEIPEEYLQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.16
R work: 0.1207
R free: 0.1383
Average B factor: 22
Crystallization pH: 7.5
Crystal growth procedure: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5
Matthews coefficient: 2.49
Solvent content (%): 50.57
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: 2015-08-26
MTH1 substrate recognition: Complex with a methylaminopurinone (PDB entry 5FSL)
Macromolecule: 7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.24
R work: 0.2015
R free: 0.2115
Average B factor: 15.92
Crystal growth procedure: 25% (W/V) PEG3350 200MM LITHIUM SULPHATE 100MM SODIUM ACETATE PH4.5
Matthews coefficient: 2.01
Solvent content (%): 38.74
Ligand: 9-METHYL-2-(METHYLAMINO)-1H-PURIN-6-ONE (UAN)
Ligand formula: C7 H9 N5 O
Ligand molecular weight: 179.179
Ligand SMILES: CNC1=Nc2c(ncn2C)C(=O)N1
Ligand InChI: InChI=1S/C7H9N5O/c1-8-7-10-5-4(6(13)11-7)9-3-12(5)2/h3H,1-2H3,(H2,8,10,11,13)
Release date: 2016-07-20
Crystal structure of the FLT3 kinase bound to a small molecule inhibitor (PDB entry 6IL3)
Macromolecule: Receptor-type tyrosine-protein kinase FLT3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 370 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQSIAHKYKKQFRYESQLQMVQVTGSSDNEYFYVDFREYEYDLKWEFPRENLEFGKVLGSGAFGKVMNATAYGISKTGVSIQVAVKMLKEKADSSEREALMSELKMMTQLGSHENIVNLLGACTLSGPIYLIFEYCCYGDLLNYLRSKREKFSEDEIEYENQKRLEEEEDLNVLTFEDLLCFAYQVAKGMEFLEFKSCVHRDLAARNVLVTHGKVVKICDFGLARDIMSDSNYVVRGNARLPVKWMAPESLFEGIYTIKSDVWSYGILLWEIFSLGVNPYPGIPVDANFYKLIQNGFKMDQPFYATEEIYIIMQSCWAFDSRKRPSFPNLTSFLGCQLADAEEAMYQNV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.183
R free: 0.21863
Average B factor: 60.251
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 10.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Lithium Sulfate, 0.1 M CAPS, pH 10.5, 1.2 M Sodium dihydrogen phosphate, 0.8 M Di-potassium hydrogen phosphate
Matthews coefficient: 2.86
Solvent content (%): 57.02
Ligand: 7-methoxy-6-(1-methyl-1H-pyrazol-4-yl)-3-(pyridin-2-yl)imidazo[1,2-a]pyridine (A9R)
Ligand formula: C17 H15 N5 O
Ligand molecular weight: 305.334
Ligand SMILES: Cn1cc(cn1)c2cn3c(cc2OC)ncc3c4ccccn4
Ligand InChI: InChI=1S/C17H15N5O/c1-21-10-12(8-20-21)13-11-22-15(14-5-3-4-6-18-14)9-19-17(22)7-16(13)23-2/h3-11H,1-2H3
Release date: 2018-12-12
Human PARP10 (ARTD10), catalytic fragment in complex with 3-aminobenzamide and citrate (PDB entry 6FXI)
Macromolecule: Poly [ADP-ribose] polymerase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 191 residues
Sequence: SMNLERLAENTGEFQEVVRAFYDTLDAARSSIRVVRVERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAHGFNRSFCGRNATVYGKGVYFARRASLSVQDRYSPPNADGHKAVFVARVLTGDYGQGRRGLRAPPLRGPGHVLLRYDSAVDCICQPSIFVIFHDTQALPTHLITCEHV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.21
R free: 0.245
Average B factor: 36.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 277
Crystal growth procedure: 16% PEG3350, 0.1 M Citrate-Bis-Tris-Propane, 3 mM 3-aminobenzamide
Matthews coefficient: 2.87
Solvent content (%): 57.1
Ligand: 3-aminobenzamide (3AB)
Ligand formula: C7 H8 N2 O
Ligand molecular weight: 136.151
Ligand SMILES: c1cc(cc(c1)N)C(=O)N
Ligand InChI: InChI=1S/C7H8N2O/c8-6-3-1-2-5(4-6)7(9)10/h1-4H,8H2,(H2,9,10)
Release date: 2019-03-20
Crystal structure of GNE-1952 alkylated KRAS G12C in complex with 2H11 CLAMP (PDB entry 7RP3)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 171 residues
Sequence: GSSTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1907
R free: 0.2339
Average B factor: 51.3508
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 0.10% n-Octyl-B-D-glucoside, 0.1 M sodium citrate pH 5.5, 22% PEG 3350
Matthews coefficient: 2.51
Solvent content (%): 50.91
Ligand: 1-[4-[6-chloranyl-7-(5-methyl-1~{H}-indazol-4-yl)quinazolin-4-yl]piperazin-1-yl]propan-1-one (MKZ)
Ligand formula: C23 H23 Cl N6 O
Ligand molecular weight: 434.921
Ligand SMILES: CCC(=O)N1CCN(CC1)c2c3cc(c(cc3ncn2)c4c(ccc5c4cn[nH]5)C)Cl
Ligand InChI: InChI=1S/C23H23ClN6O/c1-3-21(31)29-6-8-30(9-7-29)23-16-10-18(24)15(11-20(16)25-13-26-23)22-14(2)4-5-19-17(22)12-27-28-19/h4-5,10-13H,3,6-9H2,1-2H3,(H,27,28)
Release date: 2022-03-16
pUbl depleted phospho-Parkin(K211N,R163D) in complex with pUb (PDB entry 8IKV)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.31
Sequence length: 327 residues
Sequence: GPSIYNSFYVYCKGPCQRVQPGKLDVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFNCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDCRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1981
R free: 0.2169
Average B factor: 44.93
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
Matthews coefficient: 2.16
Solvent content (%): 43.16
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: 2024-09-11