satarupa22/MacromolecularLigandDB huggingface dataset:
The co-crystal structure of DYRK2 with a small molecule inhibitor 20 (PDB entry 7DHN)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 324 residues
Sequence: HDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.1853
R free: 0.2232
Average B factor: 66.7205
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.36 M-0.5 M sodium citrate tribasic dehydrate, 0.01M sodium borate, pH 7.5-9.5
Matthews coefficient: 3.63
Solvent content (%): 66.14
Ligand: 7-methoxy-2-methylsulfanyl-9-(piperidin-4-ylmethylsulfanyl)-[1,3]thiazolo[5,4-b]quinoline (H7R)
Ligand formula: C18 H21 N3 O S3
Ligand molecular weight: 391.574
Ligand SMILES: COc1ccc2c(c1)c(c3c(n2)sc(n3)SC)SCC4CCNCC4
Ligand InChI: InChI=1S/C18H21N3OS3/c1-22-12-3-4-14-13(9-12)16(24-10-11-5-7-19-8-6-11)15-17(20-14)25-18(21-15)23-2/h3-4,9,11,19H,5-8,10H2,1-2H3
Release date: 2021-11-17
Crystal structure of JAK3 in complex with FM601 (compound 10a) (PDB entry 7APF)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 294 residues
Sequence: SMQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRALAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2035
R free: 0.2549
Average B factor: 33.379
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 25% PEG 3350, 0.1-0.2 M MgCl2, 0.1 M MES, pH 5.5
Matthews coefficient: 1.98
Solvent content (%): 37.91
Ligand: 3-[3-(propanoylamino)phenyl]-1~{H}-pyrrolo[2,3-b]pyridine-5-carboxamide (RQZ)
Ligand formula: C17 H16 N4 O2
Ligand molecular weight: 308.335
Ligand SMILES: CCC(=O)Nc1cccc(c1)c2c[nH]c3c2cc(cn3)C(=O)N
Ligand InChI: InChI=1S/C17H16N4O2/c1-2-15(22)21-12-5-3-4-10(6-12)14-9-20-17-13(14)7-11(8-19-17)16(18)23/h3-9H,2H2,1H3,(H2,18,23)(H,19,20)(H,21,22)
Release date: 2020-12-02
Potent, Reversible MetAP2 Inhibitors via FBDD (PDB entry 5JI6)
Macromolecule: Methionine aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 369 residues
Sequence: KVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1821
R free: 0.2297
Average B factor: 54.495
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.9
Crystallization temperature (K): 293
Crystal growth procedure: 24.% PEG MME 2000, 0.05M MES pH 5.9, 0.0175M Ammonium Sulfate
Matthews coefficient: 2.68
Solvent content (%): 54.06
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: 2016-05-25
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1103351268 (PDB entry 5RWV)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1778
R free: 0.2017
Average B factor: 16.719
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.09
Solvent content (%): 41.13
Ligand: 2-methyl-1-[(oxan-4-yl)amino]propan-2-ol (WND)
Ligand formula: C9 H19 N O2
Ligand molecular weight: 173.253
Ligand SMILES: CC(C)(CNC1CCOCC1)O
Ligand InChI: InChI=1S/C9H19NO2/c1-9(2,11)7-10-8-3-5-12-6-4-8/h8,10-11H,3-7H2,1-2H3
Release date: 2020-11-11
Crystal structure of human IRE1 cytoplasmic kinase-RNase region - apo (PDB entry 4Z7G)
Macromolecule: Serine/threonine-protein kinase/endoribonuclease IRE1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 416 residues
Sequence: SVVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLQQTTSGLAHLHSLNIVHRDLKPHNILISMPNAHGKIKAMISDFGLCKKLAVGRHSFSRRSGVPGTEGWIAPEMLSEDCKENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQANILLGACSLDCLHPEKHEDVIARELIEKMIAMDPQKRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYFTSRFPHLLAHTYRAMELCSHERLFQPYYFHEPPEPQPPVTPDAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.203
R free: 0.2259
Average B factor: 100.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Apo-hIRE1 was crystallized by hanging-drop vapor diffusion by mixing IRE1 (at 2 mg/mL) with reservoir solution containing 18-20% PEG3350, 0.2 M sodium malonate and 0.1 Bis-Trispropane (pH 6.5) in a 1:1 ratio
Matthews coefficient: 2.8
Solvent content (%): 56.08
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-05-27
Crystal structure of Aurora-A L210C catalytic domain in complex with ASDO6 ligand (PDB entry 6HJJ)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLICEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNAQNKESASKQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.2088
R free: 0.2692
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.2 M lithium sulfate,
0.1 M sodium acetate pH 4.5, 50 % w/v polyethylene glycol 400;
Matthews coefficient: 2.55
Solvent content (%): 51.76
Ligand: ~{N}-[4-(4-azanyl-1-propan-2-yl-pyrazolo[3,4-d]pyrimidin-3-yl)-3-methyl-phenyl]-4-[4-fluoranyl-3-(trifluoromethyl)phenyl]-4-oxidanylidene-butanamide (G7T)
Ligand formula: C26 H24 F4 N6 O2
Ligand molecular weight: 528.501
Ligand SMILES: Cc1cc(ccc1c2c3c(ncnc3n(n2)C(C)C)N)NC(=O)CCC(=O)c4ccc(c(c4)C(F)(F)F)F
Ligand InChI: InChI=1S/C26H24F4N6O2/c1-13(2)36-25-22(24(31)32-12-33-25)23(35-36)17-6-5-16(10-14(17)3)34-21(38)9-8-20(37)15-4-7-19(27)18(11-15)26(28,29)30/h4-7,10-13H,8-9H2,1-3H3,(H,34,38)(H2,31,32,33)
Release date: 2018-10-03
OTUB2 in covalent complex with LN5P45 (PDB entry 8CMS)
Macromolecule: Ubiquitin thioesterase OTUB2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 236 residues
Sequence: GPMSETSFNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDGNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYAADKH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.2099
R free: 0.2521
Average B factor: 25.72
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20 %v/v 2-Propanol 
13 %w/v PEG 4K 
0.1 M HEPES pH 8
Matthews coefficient: 2.27
Solvent content (%): 45.79
Ligand: (1~{S},2~{S})-~{N}'-ethanoyl-2-(3-methylphenyl)cyclopropane-1-carbohydrazide (V2X)
Ligand formula: C13 H16 N2 O2
Ligand molecular weight: 232.278
Ligand SMILES: Cc1cccc(c1)C2CC2C(=O)NNC(=O)C
Ligand InChI: InChI=1S/C13H16N2O2/c1-8-4-3-5-10(6-8)11-7-12(11)13(17)15-14-9(2)16/h3-6,11-12H,7H2,1-2H3,(H,14,16)(H,15,17)/t11-,12+/m1/s1
Release date: 2023-11-15
Human DNA polymerase eta-DNA ternary complex: ground state at pH7.0 (K+ MES) with 1 Ca2+ ion (PDB entry 5KFA)
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): 1.51
R work: 0.1728
R free: 0.2027
Average B factor: 21.8471
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 (%): 41.44
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: 2016-06-22
Crystal structure of TTBK1 in complex with compound 10 (7-009) (PDB entry 7ZHQ)
Macromolecule: Tau-tubulin kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 309 residues
Sequence: MNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1738
R free: 0.2117
Average B factor: 25.998
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 14-23% PEG 3350, 0.2 M sodium acetate pH 7.0 and 0.1 M tris pH 7.5-9.0
Matthews coefficient: 2.3
Solvent content (%): 46.63
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2023-04-19
Human cyclic GMP-AMP synthase (cGAS) in complex with 3',3'-cdUMP (PDB entry 5VDS)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 363 residues
Sequence: MGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.766
R work: 0.206
R free: 0.2451
Average B factor: 53.5442
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 18-20% PEG 3350, 0.2 M ammonium citrate pH 7
Matthews coefficient: 2.56
Solvent content (%): 51.95
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: 2017-09-27
Crystal Structure of CYP2B6 (Y226H/K262R) in complex with myrtenyl bromide. (PDB entry 5UEC)
Macromolecule: Cytochrome P450 2B6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.13
Sequence length: 476 residues
Sequence: MAKKTSSKGKLPPGPRPLPLLGNLLQMDRRGLLKSFLRFREKYGDVFTVHLGPRPVVMLCGVEAIREALVDKAEAFSGRGKIAMVDPFFRGYGVIFANGNRWKVLRRFSVTTMRDFGMGKRSVEERIQEEAQCLIEELRKSKGALMDPTFLFQSITANIICSIVFGKRFHYQDQEFLKMLNLFYQTFSLISSVFGQLFELFSGFLKHFPGAHRQVYKNLQEINAYIGHSVEKHRETLDPSAPRDLIDTYLLHMEKEKSNAHSEFSHQNLNLNTLSLFFAGTETTSTTLRYGFLLMLKYPHVAERVYREIEQVIGPHRPPELHDRAKMPYTEAVIYEIQRFSDLLPMGVPHIVTQHTSFRGYIIPKDTEVFLILSTALHDPHYFEKPDAFNPDHFLDANGALKKTEAFIPFSLGKRICLGEGIARAELFLFFTTILQNFSMASPVAPEDIDLTPQECGVGKIPPTYQIRFLPRHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.17421
R free: 0.22893
Average B factor: 48.561
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Magnesium acetate tetrahydrate
25%w/v PEG3350
Matthews coefficient: 3.2
Solvent content (%): 61.52
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: 2017-04-12
CBP in complex with Cpd23 ((R)-6-(3-(benzyloxy)phenyl)-4-methyl-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one) (PDB entry 5I8B)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 264 residues
Sequence: MHHHHHHGSLVPRGSMDYKDDDDKENLYFQGSRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLGYCCGRKYEFSPQTLCCYGKQLCTIPRDAAYYSYQNRYHFCEKCFTEIQGENVTLGDDPSQPQTTISKDQFEKKKNDTLDPEPFVDCKECGRKMHQICVLHYDIIWPSGFVCDNCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5218
R work: 0.1898
R free: 0.2002
Average B factor: 38.3686
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris pH 8,
 0.2 M sodium thiocyanate 
19-23% PEG 3350
Matthews coefficient: 2.36
Solvent content (%): 47.94
Ligand: (4R)-6-[3-(benzyloxy)phenyl]-4-methyl-1,3,4,5-tetrahydro-2H-1,5-benzodiazepin-2-one (69F)
Ligand formula: C23 H22 N2 O2
Ligand molecular weight: 358.433
Ligand SMILES: CC1CC(=O)Nc2cccc(c2N1)c3cccc(c3)OCc4ccccc4
Ligand InChI: InChI=1S/C23H22N2O2/c1-16-13-22(26)25-21-12-6-11-20(23(21)24-16)18-9-5-10-19(14-18)27-15-17-7-3-2-4-8-17/h2-12,14,16,24H,13,15H2,1H3,(H,25,26)/t16-/m1/s1
Release date: 2016-04-20
Structure of phosphomimetic Rab8a GTPase (T72E) in the GTP-bound state (PDB entry 6WHE)
Macromolecule: Ras-related protein Rab-8A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 184 residues
Sequence: GSHMAKTYDYLFKLLLIGDSGVGKTCVLFRFSEDAFNSTFISTIGIDFKIRTIELDGKRIKLQIWDTAGLERFREITTAYYRGAMGIMLVYDITNEKSFDNIRNWIRNIEEHASADVEKMILGNKCDVNDKRQVSKERGEKLALDYGIKFMETSAKANINVENAFFTLARDIKAKMDKKLEGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.1866
R free: 0.2304
Average B factor: 19.8405
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 289
Crystal growth procedure: 20% PEG3350,
0.1M Hepes pH 7
Matthews coefficient: 1.96
Solvent content (%): 37.35
Ligand: GUANOSINE-5'-TRIPHOSPHATE (GTP)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2021-03-10
Co-crystal structure of the FK506 binding domain of human FKBP25, Rapamycin and the FRB domain of human mTOR (PDB entry 5GPG)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 117 residues
Sequence: SPKYTKSVLKKGDKTNFPKKGDVVHCWYTGTLQDGTVFDTNIQTSAKKKKNAKPLSFKVGVGKVIRGWDEALLTMSKGEKARLEIEPEWAYGKKGQPDAKIPPNAKLTFEVELVDID
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.174
R free: 0.212
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% polyethyleneglycol 8000, 100mM sodium cacodylate, 200mM sodium acetate, 10mM manganese chloride
Matthews coefficient: 2.47
Solvent content (%): 50.2
Ligand: RAPAMYCIN IMMUNOSUPPRESSANT DRUG (RAP)
Ligand formula: C51 H79 N O13
Ligand molecular weight: 914.172
Ligand SMILES: CC1CCC2CC(C(=CC=CC=CC(CC(C(=O)C(C(C(=CC(C(=O)CC(OC(=O)C3CCCCN3C(=O)C(=O)C1(O2)O)C(C)CC4CCC(C(C4)OC)O)C)C)O)OC)C)C)C)OC
Ligand InChI: InChI=1S/C51H79NO13/c1-30-16-12-11-13-17-31(2)42(61-8)28-38-21-19-36(7)51(60,65-38)48(57)49(58)52-23-15-14-18-39(52)50(59)64-43(33(4)26-37-20-22-40(53)44(27-37)62-9)29-41(54)32(3)25-35(6)46(56)47(63-10)45(55)34(5)24-30/h11-13,16-17,25,30,32-34,36-40,42-44,46-47,53,56,60H,14-15,18-24,26-29H2,1-10H3/b13-11+,16-12+,31-17+,35-25+/t30-,32-,33-,34-,36-,37+,38+,39+,40-,42+,43+,44-,46-,47+,51-/m1/s1
Release date: 2016-10-12
Crystal structure of USP7 in complex with allosteric inhibitor FX1-3763 (PDB entry 8D4Z)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 361 residues
Sequence: MSKKHTGYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSDKPVGTKKLTKSFGWETLDSFMQHDVQELCRVLLDNVENKMKGTCVEGTIPKLFRGKMVSYIQCKEVDYRSDRREDYYDIQLSIKGKKNIFESFVDYVAVEQLDGDNKYDAGEHGLQEAEKGVKFLTLPPVLHLQLMRFMYDPQTDQNIKINDRFEFPEQLPLDEFLQKTDPKDPANYILHAVLVHSGDNHGGHYVVYLNPKGDGKWCKFDDDVVSRCTKEEAIEHNYGGHDDDLSVRHCTNAYMLVYIRESKLSEVLQAVTDHDIPQQLVERLQEEKRIEAQKRKERQEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.203
R free: 0.26
Average B factor: 69.1612
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M Bis-Tris-Propane pH 8.50, 0.10 M K-formate, 26.0 % (w/v) PEG 3350
Matthews coefficient: 2.32
Solvent content (%): 46.97
Ligand: 1-({(7M)-7-[1-(azetidin-3-yl)-6-chloro-1,2,3,4-tetrahydroquinolin-8-yl]thieno[3,2-b]pyridin-2-yl}methyl)pyrrolidine-2,5-dione (QBL)
Ligand formula: C24 H23 Cl N4 O2 S
Ligand molecular weight: 466.983
Ligand SMILES: c1cnc2cc(sc2c1c3cc(cc4c3N(CCC4)C5CNC5)Cl)CN6C(=O)CCC6=O
Ligand InChI: InChI=1S/C24H23ClN4O2S/c25-15-8-14-2-1-7-28(16-11-26-12-16)23(14)19(9-15)18-5-6-27-20-10-17(32-24(18)20)13-29-21(30)3-4-22(29)31/h5-6,8-10,16,26H,1-4,7,11-13H2
Release date: 2023-09-20
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000294a (PDB entry 5QDG)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1801
R free: 0.2069
Average B factor: 38.952
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.03
Ligand: 8-[(dimethylamino)methyl]-4-methyl-7-oxidanyl-chromen-2-one (AWS)
Ligand formula: C13 H15 N O3
Ligand molecular weight: 233.263
Ligand SMILES: CC1=CC(=O)Oc2c1ccc(c2CN(C)C)O
Ligand InChI: InChI=1S/C13H15NO3/c1-8-6-12(16)17-13-9(8)4-5-11(15)10(13)7-14(2)3/h4-6,15H,7H2,1-3H3
Release date: 2018-10-10
LSD1-CoREST-S2101 N5 adduct model (PDB entry 6KGL)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1772
R free: 0.2048
Average B factor: 92.34
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate
Matthews coefficient: 6.93
Solvent content (%): 82.25
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: 2020-03-25