satarupa22/MacromolecularLigandDB huggingface dataset:
Human Cytochrome P450 2D6 Quinine Complex (PDB entry 4WNV)
Macromolecule: Cytochrome P450 2D6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.1
Sequence length: 479 residues
Sequence: MAKKTSSKGKLPPGPLPLPGLGNLLHVDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREALVTHGEDTADRPPVPITQILGFGPRSQGVFLARYGPAWREQRRFSVSTLRNLGLGKKSLEQWVTEEAACLCAAFANHSGRPFRPNGLLDKAVSNVIASLTCGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLLHIPALAGKVLRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAEMEKAKGNPESSFNDENLRIVVADLFSAGMVTTSTTLAWGLLLMILHPDVQRRVQQEIDDVIGQVRRPEMGDQAHMPYTTAVIHEVQRFGDIVPLGVTHMTSRDIEVQGFRIPKGTTLITNLSSVLKDEAVWEKPFRFHPEHFLDAQGHFVKPEAFLPFSAGRRACLGEPLARMELFLFFTSLLQHFSFSVPTGQPRPSHHGVFAFLVSPSPYELCAVPRHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2022
R free: 0.2382
Average B factor: 35.4643
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: PEG3350, SODIUM ACETATE, SODIUM CACODYLATE, POTASSIUM PHOSPHATE, SODIUM CHLORIDE, ZINC CHLORIDE, GLYCEROL, BETA-MERCAPTOETHANOL, THIORIDAZINE, HEGA-10, FACIAL AMPHIPHILE 231_CHOL. Quinine was added to the mother liquor after crystallization of the P450 2D6 thiordidazine complex.
Matthews coefficient: 3.22
Solvent content (%): 61.81
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2015-01-14
CRYSTAL STRUCTURE OF CSN5(2-257) IN COMPLEX WITH CNS5i-3 (PDB entry 5JOG)
Macromolecule: COP9 signalosome complex subunit 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4
Sequence length: 257 residues
Sequence: GAASGSGMAQKTWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKMVMHARSGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSHPGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNKIEDFGVHCKQYYALEVSYFKSSLDRKLLELLWNKYWVNTLSSSSLLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.208
R free: 0.243
Average B factor: 82.25
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Protein solution: 18.9 mg/ml protein in 50mM NaCl, 50mM Mes/NaOH pH 6.0, 10uM ZnCl2, 0.5 mM TCEP with 1mM compound
Crystallization solution: 35% MPD, 0.1M MES/NaOH pH 6.0, 0.2 M Li2SO4
Matthews coefficient: 3.04
Solvent content (%): 59.58
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: 2016-11-02
Crystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61) (PDB entry 6ZKW)
Macromolecule: HLA class I histocompatibility antigen, alpha chain E
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 276 residues
Sequence: GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLLHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP
Oligomeric state: Hetero 5-mer
Stoichiometry: A1, B1, C1, D1, E1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.24291
R free: 0.28706
Average B factor: 61.858
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M TRIS pH 8.5, 25 % (w/v) PEG 4000, 15 % Glycerol
Matthews coefficient: 2.47
Solvent content (%): 50.3
Release date: 2022-01-26
human GUK1 in complex with compound AT8001 (PDB entry 8PTS)
Macromolecule: Guanylate kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.8
Sequence length: 197 residues
Sequence: MSGPRPVVLSGPSGAGKSTLLKRLLQEHSGIFGFSVSHTTRNPRPGEENGKDYYFVTREVMQRDIAAGDFIEHAEFSGNLYGTSKVAVQAVQAMNRICVLDVDLQGVRNIKATDLRPIYISVQPPSLHVLEQRLRQRNTETEESLVKRLAAAQADMESSKEPGLFDVVIINDSLDQAYAELKEALSEEIKKAQRTGA
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.2481
R free: 0.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 12 -17 % PEG330
66mM Na Cacodylate
33mM MES
66mM MgCl2
Matthews coefficient: 2.31
Solvent content (%): 46.78
Ligand: [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate (EIF)
Ligand formula: C11 H15 F N5 O7 P
Ligand molecular weight: 379.238
Ligand SMILES: CC1(C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)O)O)F
Ligand InChI: InChI=1S/C11H15FN5O7P/c1-11(12)6(18)4(2-23-25(20,21)22)24-9(11)17-3-14-5-7(17)15-10(13)16-8(5)19/h3-4,6,9,18H,2H2,1H3,(H2,20,21,22)(H3,13,15,16,19)/t4-,6-,9-,11-/m1/s1
Release date: 2024-07-24
Human cathepsin K mutant C25S in complex with the allosteric effector NSC94914 (PDB entry 5JA7)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 223 residues
Sequence: YIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSSWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.1808
R free: 0.2201
Average B factor: 18.4998
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonium sulfate, 30% (w/v) PEG-8000
Matthews coefficient: 2.12
Solvent content (%): 41.99
Ligand: [([1,1'-biphenyl]-2-yl)methyl]propanedioic acid (6HM)
Ligand formula: C16 H14 O4
Ligand molecular weight: 270.28
Ligand SMILES: c1ccc(cc1)c2ccccc2CC(C(=O)O)C(=O)O
Ligand InChI: InChI=1S/C16H14O4/c17-15(18)14(16(19)20)10-12-8-4-5-9-13(12)11-6-2-1-3-7-11/h1-9,14H,10H2,(H,17,18)(H,19,20)
Release date: 2016-11-30
MEK1 in complex with compound 23 (PDB entry 7B9L)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 1,Dual specificity mitogen-activated protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 326 residues
Sequence: MAHHHHHHAAAENLYFQLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIGSGSGSMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.193
R free: 0.214
Average B factor: 40.17
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Crystals were obtained from hanging drops by mixing a 1:1 ratio of protein solution with well solution containing 2 M AmSO4, 0.1 M NaCl and 0.1 M Bis-tris pH 6.1-6.2
Matthews coefficient: 2.26
Solvent content (%): 45.55
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: 2021-03-03
Structure of HDAC2 complexed with an inhibitory ligand (PDB entry 7ZZP)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 498 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPHAPGVQMQAIPEDAVHEDSGDEDGEDPDKRISIRASDKRIACDEEFSDSEDEGEGGRRNVADHKKGAKKARIEEDKKETEDKKTDVKEEDKSKDNSGEKTDTKGTKSEQLSNPGSSGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.1531
R free: 0.1736
Average B factor: 22.558
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 39% PEG 300
0.1M pH=8.4 CHES/NaOH
Matthews coefficient: 1.91
Solvent content (%): 35.66
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-09-21
Tricomplex of RMC-7977, KRAS G12V, and CypA (PDB entry 8TBM)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: SMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1782
R free: 0.2107
Average B factor: 30.24
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 24% PEG6000, 0.1 M imidazole, pH 7
Matthews coefficient: 2.33
Solvent content (%): 47.3
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2024-02-07
Crystal Structure of Recombinant GBA in Complex with Bis-Tris Propane. (PDB entry 6TJK)
Macromolecule: Lysosomal acid glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 497 residues
Sequence: ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1646
R free: 0.1985
Average B factor: 22.553
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Na2SO4, 14% (v/v) PEG3350, 0.1 M bis-tris-propane pH 7.0
Matthews coefficient: 2.47
Solvent content (%): 50.14
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: 2020-06-10
Crystal structure of human tryptophan hydroxylase 1 in complex with inhibitor TPT-004 (PDB entry 8CJL)
Macromolecule: Tryptophan 5-hydroxylase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.4
Sequence length: 326 residues
Sequence: MKHHHHHHHGAAGTSLYKKAGENLYFQGSVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.1951
R free: 0.225
Average B factor: 33.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 18% PEG6000, 0.1 M Tris pH 8.5
Matthews coefficient: 2.32
Solvent content (%): 46.97
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2024-01-10
Crystal structure of the human METTL3-METTL14 complex bound to Compound 22 (UZH2) (PDB entry 7O2F)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1971
R free: 0.2421
Average B factor: 40.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.18
Solvent content (%): 43.52
Ligand: 4-[4-[(4,4-dimethylpiperidin-1-yl)methyl]-2,5-bis(fluoranyl)phenyl]-9-[6-(methylamino)pyrimidin-4-yl]-1,4,9-triazaspiro[5.5]undecan-2-one (UZ5)
Ligand formula: C27 H37 F2 N7 O
Ligand molecular weight: 513.626
Ligand SMILES: CC1(CCN(CC1)Cc2cc(c(cc2F)N3CC(=O)NC4(C3)CCN(CC4)c5cc(ncn5)NC)F)C
Ligand InChI: InChI=1S/C27H37F2N7O/c1-26(2)4-8-34(9-5-26)15-19-12-21(29)22(13-20(19)28)36-16-25(37)33-27(17-36)6-10-35(11-7-27)24-14-23(30-3)31-18-32-24/h12-14,18H,4-11,15-17H2,1-3H3,(H,33,37)(H,30,31,32)
Release date: 2021-09-01
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13371a (PDB entry 5R50)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1793
R free: 0.233
Average B factor: 29.098
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.03
Solvent content (%): 39.37
Ligand: N-[4-(aminomethyl)phenyl]methanesulfonamide (RY4)
Ligand formula: C8 H12 N2 O2 S
Ligand molecular weight: 200.258
Ligand SMILES: CS(=O)(=O)Nc1ccc(cc1)CN
Ligand InChI: InChI=1S/C8H12N2O2S/c1-13(11,12)10-8-4-2-7(6-9)3-5-8/h2-5,10H,6,9H2,1H3
Release date: 2020-07-01
An open conformation Form2 of switch II for RhoA GDP-bound state (PDB entry 7WZC)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: YFQGMAAIRKKLVIVGDGAVGKTSLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMVFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMETSAKTKDGVREVFEMATRAALQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7994492129
R work: 0.204621538564
R free: 0.264065073643
Average B factor: 22.7305161955
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.1M MES, pH6.0, 30% PEG 600, 5% PEG 1000, 10% glycerol
Matthews coefficient: 2.08
Solvent content (%): 40.86
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: 2023-02-22
Notum complex with ARUK3003910 (PDB entry 7B2Y)
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): 1.23
R work: 0.1863
R free: 0.2076
Average B factor: 22.9289
Crystallization method: EVAPORATION
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate
Matthews coefficient: 1.92
Solvent content (%): 36.01
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: 2021-08-04
Structure of human NNMT in complex with macrocyclic peptide 2 (PDB entry 7EHZ)
Macromolecule: Nicotinamide N-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.1
Sequence length: 259 residues
Sequence: GSGFTSKDTYLSHFNPRDYLEKYYKFGSRHSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKKEPAAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKSSYYMIGEQKFSSLPLGREAVEAAVKEAGYTIEWFEVISQSYSSTMANNEGLFSLVARKL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1933
R free: 0.2552
Average B factor: 49.802
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Bicine pH9.0, 20% w/v PEG 6000
Matthews coefficient: 2.16
Solvent content (%): 42.97
Release date: 2021-12-15
Structure of human beta1 adrenergic receptor bound to BI-167107 and nanobody 6B9 (PDB entry 7BU7)
Macromolecule: Endolysin,Endolysin,Beta-1 adrenergic receptor chimera
Type: Protein, polypeptide(L)
Source organism: Tequatrovirus T4
EC number: 3.2.1.17
Sequence length: 516 residues
Sequence: DYKDDDDANIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAASQQWTAGMGLLMALIVLLIVAGNVLVIVAIAKTPRLQTLTNLFIMSLASADLVMGLLVVPFGATIVVWGRWEYGSFFCELWTSVDVLCVTASIETLCVIALDRYLAITSPFRYQSLLTRARARGLVCTVWAISALVSFLPILMHWWRAESDEARRCYNDPKCCDFVTNRAYAIASSVVSFYVPLCIMAFVYLRVFREAQKQVKKIDSCERRFLGGPARPPSPSPSPVPAPAPPPGPPRPAAAAATAPLANGRAGKRRPSRLVALREQKALKTLGIIMGVFTLCWLPFFLANVVKAFHRELVPDRLFVFFNWLGYANSAFNPIIYCRSPDFRKAFQGLLCCARRAAR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2435
R free: 0.2698
Average B factor: 83.32
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES, pH 7.5, 100-175mM (NH4)2SO4, 38-43% PEG400, 0.15M-0.2M Glycine
Matthews coefficient: 4.51
Solvent content (%): 72.73
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: 2020-12-02
Crystal structure of USP7 in complex with the covalent inhibitor, FT827 (PDB entry 5NGF)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 355 residues
Sequence: GSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQKRKERQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.18802
R free: 0.2469
Average B factor: 73.06
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 7.5, 0.2 M sodium formate
Matthews coefficient: 2.5
Solvent content (%): 50.88
Ligand: ~{N}-[2-[4-[4-[(1-methyl-4-oxidanylidene-pyrazolo[3,4-d]pyrimidin-5-yl)methyl]-4-oxidanyl-piperidin-1-yl]carbonylphenyl]phenyl]ethanesulfonamide (8WN)
Ligand formula: C27 H30 N6 O5 S
Ligand molecular weight: 550.629
Ligand SMILES: CCS(=O)(=O)Nc1ccccc1c2ccc(cc2)C(=O)N3CCC(CC3)(CN4C=Nc5c(cnn5C)C4=O)O
Ligand InChI: InChI=1S/C27H30N6O5S/c1-3-39(37,38)30-23-7-5-4-6-21(23)19-8-10-20(11-9-19)25(34)32-14-12-27(36,13-15-32)17-33-18-28-24-22(26(33)35)16-29-31(24)2/h4-11,16,18,30,36H,3,12-15,17H2,1-2H3
Release date: 2017-10-18
Crystal structure of LSD2 in complex with cis-4-Br-PCPA (PDB entry 7XE1)
Macromolecule: Lysine-specific histone demethylase 1B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 793 residues
Sequence: AKKKATETTDEDEDGGSEKKYRKCEKAGCTATCPVCFASASERCAKNGYTSRWYHLSCGEHFCNECFDHYYRSHKDGYDKYTTWKKIWTSNGKTEPSPKAFMADQQLPYWVQCTKPECRKWRQLTKEIQLTPQIAKTYRCGMKPNTAIKPETSDHCSLPEDLRVLEVSNHWWYSMLILPPLLKDSVAAPLLSAYYPDCVGMSPSCTSTNRAAATGNASPGKLEHSKAALSVHVPGMNRYFQPFYQPNECGKALCVRPDVMELDELYEFPEYSRDPTMYLALRNLILALWYTNCKEALTPQKCIPHIIVRGLVRIRCVQEVERILYFMTRKGLINTGVLSVGADQYLLPKDYHNKSVIIIGAGPAGLAAARQLHNFGIKVTVLEAKDRIGGRVWDDKSFKGVTVGRGAQIVNGCINNPVALMCEQLGISMHKFGERCDLIQEGGRITDPTIDKRMDFHFNALLDVVSEWRKDKTQLQDVPLGEKIEEIYKAFIKESGIQFSELEGQVLQFHLSNLEYACGSNLHQVSARSWDHNEFFAQFAGDHTLLTPGYSVIIEKLAEGLDIQLKSPVQCIDYSGDEVQVTTTDGTGYSAQKVLVTVPLALLQKGAIQFNPPLSEKKMKAINSLGAGIIEKIALQFPYRFWDSKVQGADFFGHVPPSASKRGLFAVFYDMDPQKKHSVLMSVIAGEAVASVRTLDDKQVLQQCMATLRELFKEQEVPDPTKYFVTRWSTDPWIQMAYSFVKTGGSGEAYDIIAEDIQGTVFFAGEATNRHFPQTVTGAYLSGVREASKIAAF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.164
R free: 0.192
Average B factor: 46.32
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 320mM Ammonium citrate, 22% PEG 3350
Matthews coefficient: 3.5
Solvent content (%): 64.88
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2022-09-14
Crystal structure of the human Lyn SH3 domain (PDB entry 6NMW)
Macromolecule: Tyrosine-protein kinase Lyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 69 residues
Sequence: EQGDIVVALYPYDGIHPDDLSFKKGEKMKVLEEHGEWWKAKSLLTKKEGFIPSNYVAKLNTLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.199
R work: 0.1725
R free: 0.1827
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Na citrate, 3.2 M NaCl
Matthews coefficient: 2.22
Solvent content (%): 44.71
Release date: 2019-04-17