satarupa22/MacromolecularLigandDB huggingface dataset:
Human SIRT3 in complex with halistanol sulfate (PDB entry 5Y4H)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 285 residues
Sequence: SNASDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.21514
R free: 0.26914
Average B factor: 61.284
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Potassium phosphate
Matthews coefficient: 2.68
Solvent content (%): 54.04
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: 2018-05-16
H. SAPIENS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5,6-DIBROMOBENZOTRIAZOLE AT PH 5.5 (PDB entry 7QGC)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 399 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.1705
R free: 0.2315
Average B factor: 42.542
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 290
Crystal growth procedure: 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 monomethyl ester, 10% polyethylene glycol 20 000, and 0.1 M buffering solution of imidazole/MES pH 6.5
Matthews coefficient: 2.68
Solvent content (%): 54.05
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2022-09-28
Crystal structure of mouse KDM2A-H3K36ME-NO complex (PDB entry 4TN7)
Macromolecule: Lysine-specific demethylase 2A
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 1.14.11.27
Sequence length: 329 residues
Sequence: RTFDLEEKLQTNKYNANFVTFMEGKDFNVEYIQRGGLRDPLIFKNSDGLGIKMPDPDFTVNDVKMCVGSRRMVDVMDVNTQKGIEMTMAQWTRYYETPEEEREKLYNVISLEFSHTRLENMVQRPSTVDFIDWVDNMWPRHLKESQTESTNAILEMQYPKVQKYCLMSVRGCYTDFHVDFGGTSVWYHIHQGGKVFWLIPPTAHNLELYENWLLSGKQGDIFLGDRVSDCQRIELKQGYTFVIPSGWIHAVYTPTDTLVFGGNFLHSFNIPMQLKIYSIEDRTRVPNKFRYPFYYEMCWYVLERYVYCITNRSHLTKDFQKESLSMDME
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2294
R free: 0.2794
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Li-citrate
18-30% PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.77
Ligand: NITRIC OXIDE (NO)
Ligand formula: N O
Ligand molecular weight: 30.006
Ligand SMILES: [N]=O
Ligand InChI: InChI=1S/HNO/c1-2/h1H
Release date: 2015-05-13
Crystal structure of haspin in complex with 5-iodotubercidin (PDB entry 6G34)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.13833
R free: 0.17374
Average B factor: 21.753
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 51-63% MPD and 0.1M SPG buffer, pH 6.0-6.5
Matthews coefficient: 3.03
Solvent content (%): 59.4
Ligand: (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL (5ID)
Ligand formula: C11 H13 I N4 O4
Ligand molecular weight: 392.15
Ligand SMILES: c1c(c2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)I
Ligand InChI: InChI=1S/C11H13IN4O4/c12-4-1-16(10-6(4)9(13)14-3-15-10)11-8(19)7(18)5(2-17)20-11/h1,3,5,7-8,11,17-19H,2H2,(H2,13,14,15)/t5-,7-,8-,11-/m1/s1
Release date: 2018-04-18
Crystal structure of CBP bromodomain liganded with 9c (PDB entry 7EVJ)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 133 residues
Sequence: MKKGHHHHHHLVPRGSRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.57
R work: 0.1869
R free: 0.2093
Average B factor: 41.498
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M NH4H2PO4, 20% PEG 3350, pH 4.6, and 20% Gly
Matthews coefficient: 2.24
Solvent content (%): 45.08
Ligand: 3-acetyl-1-((3-(1-cyclopropyl-1H-pyrazol-4-yl)-2-fluoro-5-(hydroxymethyl)phenyl)carbamoyl)indolizin-7-yl dimethylcarbamate (JE9)
Ligand formula: C27 H26 F N5 O5
Ligand molecular weight: 519.524
Ligand SMILES: CC(=O)c1cc(c2n1ccc(c2)OC(=O)N(C)C)C(=O)Nc3cc(cc(c3F)c4cnn(c4)C5CC5)CO
Ligand InChI: InChI=1S/C27H26FN5O5/c1-15(35)23-11-21(24-10-19(6-7-32(23)24)38-27(37)31(2)3)26(36)30-22-9-16(14-34)8-20(25(22)28)17-12-29-33(13-17)18-4-5-18/h6-13,18,34H,4-5,14H2,1-3H3,(H,30,36)
Release date: 2022-02-16
The co-structure of (R)-4-(6-(1-(cyclopropylsulfonyl)cyclopropyl)-2-(1H-indol-4-yl)pyrimidin-4-yl)-3-methylmorpholine and a rationally designed PI3K-alpha mutant that mimics ATR (PDB entry 5UK8)
Macromolecule: Phosphatidylinositol 3-kinase regulatory subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 293 residues
Sequence: MHNLQYLPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.198
R free: 0.24
Average B factor: 70.38
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 303.15
Crystal growth procedure: 3 UL OF PROTEIN WAS MIXED WITH 5 UL OF WELL SOLUTION CONTAINING 12% PEG 3350 AND 120 MM POTASSIUM THIOCYANATE, PH 7.2, VAPOR DIFFUSION, HANGING DROP,
TEMPERATURE   303.15K
Matthews coefficient: 2.34
Solvent content (%): 47.42
Ligand: (R)-4-(6-(1-(cyclopropylsulfonyl)cyclopropyl)-2-(1H-indol-4-yl)pyrimidin-4-yl)-3-methylmorpholine (8DV)
Ligand formula: C23 H26 N4 O3 S
Ligand molecular weight: 438.543
Ligand SMILES: CC1COCCN1c2cc(nc(n2)c3cccc4c3cc[nH]4)C5(CC5)S(=O)(=O)C6CC6
Ligand InChI: InChI=1S/C23H26N4O3S/c1-15-14-30-12-11-27(15)21-13-20(23(8-9-23)31(28,29)16-5-6-16)25-22(26-21)18-3-2-4-19-17(18)7-10-24-19/h2-4,7,10,13,15-16,24H,5-6,8-9,11-12,14H2,1H3/t15-/m1/s1
Release date: 2017-06-14
Crystal structure of KRAS G12D in complex with GDP and compound 14 (PDB entry 8TXH)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.1904
R free: 0.2033
Average B factor: 14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 286.15
Crystal growth procedure: 0.1 M Sodium Acetate pH 4.5, 40% PEG 400
Matthews coefficient: 2.17
Solvent content (%): 43.41
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2023-11-08
Linked KDM5A Jmj Domain Bound to the Inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamid (PDB entry 5IWF)
Macromolecule: Lysine-specific demethylase 5A,Lysine-specific demethylase 5A
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): 2.289
R work: 0.192
R free: 0.2435
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: 2.23
Solvent content (%): 44.87
Ligand: 2-[[[2-[2-(dimethylamino)ethyl-ethyl-amino]-2-oxidanylidene-ethyl]amino]methyl]pyridine-4-carboxamide (LQT)
Ligand formula: C15 H25 N5 O2
Ligand molecular weight: 307.391
Ligand SMILES: CCN(CCN(C)C)C(=O)CNCc1cc(ccn1)C(=O)N
Ligand InChI: InChI=1S/C15H25N5O2/c1-4-20(8-7-19(2)3)14(21)11-17-10-13-9-12(15(16)22)5-6-18-13/h5-6,9,17H,4,7-8,10-11H2,1-3H3,(H2,16,22)
Release date: 2016-07-27
Cocrystal structure of the human acyl protein thioesterase 1 with an isoform-selective inhibitor, ML348 (PDB entry 5SYM)
Macromolecule: Acyl-protein thioesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2
Sequence length: 230 residues
Sequence: MCGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPVTLNMNVAMPSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGVTALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLVNPANVTFKTYEGMMHSSCQQEMMDVKQFIDKLLPPID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.179
R free: 0.199
Average B factor: 19.12
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium citrate, 22-24% PEG 3350, 200 mM MgCl2
Matthews coefficient: 2.19
Solvent content (%): 43.77
Ligand: N-[2-chloro-5-(trifluoromethyl)phenyl]-2-[4-(furan-2-carbonyl)piperazin-1-yl]acetamide (71Q)
Ligand formula: C18 H17 Cl F3 N3 O3
Ligand molecular weight: 415.794
Ligand SMILES: c1cc(oc1)C(=O)N2CCN(CC2)CC(=O)Nc3cc(ccc3Cl)C(F)(F)F
Ligand InChI: InChI=1S/C18H17ClF3N3O3/c19-13-4-3-12(18(20,21)22)10-14(13)23-16(26)11-24-5-7-25(8-6-24)17(27)15-2-1-9-28-15/h1-4,9-10H,5-8,11H2,(H,23,26)
Release date: 2016-10-26
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z1741973467 (PDB entry 5RYA)
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): 1.32
R work: 0.1792
R free: 0.2064
Average B factor: 19.15
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: 2.08
Solvent content (%): 40.73
Ligand: (4-methoxyphenyl)(piperidin-4-yl)methanone (WKP)
Ligand formula: C13 H17 N O2
Ligand molecular weight: 219.28
Ligand SMILES: COc1ccc(cc1)C(=O)C2CCNCC2
Ligand InChI: InChI=1S/C13H17NO2/c1-16-12-4-2-10(3-5-12)13(15)11-6-8-14-9-7-11/h2-5,11,14H,6-9H2,1H3
Release date: 2020-11-11
Notum-Fragment049 (PDB entry 7B7W)
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): 1.6
R work: 0.205
R free: 0.2267
Average B factor: 25.1576
Crystallization method: EVAPORATION
Crystallization pH: 4.2
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate
Matthews coefficient: 1.96
Solvent content (%): 37.37
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2021-07-21
Human caspase-3 in complex with Ac-DW3-KE (PDB entry 6CKZ)
Macromolecule: Caspase-3 subunit p17
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 175 residues
Sequence: MENTENSVDSKSIKNLEPKIIHGSESMDSGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1531
R free: 0.1714
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.4
Crystallization temperature (K): 295
Crystal growth procedure: 1:1 dilution with 0.10 M sodium citrate, pH 5.4, 15.2 % PEG6000, 0.010 M DTT, 0.02% NaN3.
Matthews coefficient: 2.01
Solvent content (%): 38.79
Release date: 2019-03-06
Human p38alpha MAPK in complex with imidazolyl pyridine inhibitor 11b (PDB entry 5ML5)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.19293
R free: 0.23964
Average B factor: 26.764
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.2, 
20-30 % PEG4000,
50 mM BOG
Matthews coefficient: 2.07
Solvent content (%): 40.54
Ligand: octyl beta-D-glucopyranoside (BOG)
Ligand formula: C14 H28 O6
Ligand molecular weight: 292.369
Ligand SMILES: CCCCCCCCOC1C(C(C(C(O1)CO)O)O)O
Ligand InChI: InChI=1S/C14H28O6/c1-2-3-4-5-6-7-8-19-14-13(18)12(17)11(16)10(9-15)20-14/h10-18H,2-9H2,1H3/t10-,11-,12+,13-,14-/m1/s1
Release date: 2017-04-05
Crystal structure of DYRK1A in complex with CX-4945 (PDB entry 7Z5N)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 370 residues
Sequence: DSSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADEGTNTHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.77
R work: 0.205
R free: 0.2516
Average B factor: 84.9253
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0,1M TRIS pH 7.7, 0,1M Li2SO4, 40% PEG300
Matthews coefficient: 2.91
Solvent content (%): 57.76
Ligand: 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid (3NG)
Ligand formula: C19 H12 Cl N3 O2
Ligand molecular weight: 349.77
Ligand SMILES: c1cc(cc(c1)Cl)Nc2c3ccncc3c4ccc(cc4n2)C(=O)O
Ligand InChI: InChI=1S/C19H12ClN3O2/c20-12-2-1-3-13(9-12)22-18-15-6-7-21-10-16(15)14-5-4-11(19(24)25)8-17(14)23-18/h1-10H,(H,22,23)(H,24,25)
Release date: 2023-03-22
Crystal structure of DPO4 with 8-oxoadenine (oxoA) and dTTP* (PDB entry 6VGM)
Macromolecule: DNA polymerase IV
Type: Protein, polypeptide(L)
Source organism: Saccharolobus solfataricus
EC number: 2.7.7.7
Sequence length: 341 residues
Sequence: MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.84
R work: 0.2302
R free: 0.2798
Average B factor: 75.74
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM Tris
100 mM Magnesium Acetate
16% PEG 3350
Matthews coefficient: 2.67
Solvent content (%): 53.91
Ligand: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine (1FZ)
Ligand formula: C10 H18 N3 O13 P3
Ligand molecular weight: 481.184
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C10H18N3O13P3/c1-5-3-13(10(16)11-9(5)15)8-2-6(14)7(25-8)4-24-27(17,18)12-28(19,20)26-29(21,22)23/h3,6-8,14H,2,4H2,1H3,(H,11,15,16)(H2,21,22,23)(H3,12,17,18,19,20)/t6-,7+,8+/m0/s1
Release date: 2021-01-06
Crystal structure of Syk in complex with GS-9876 (PDB entry 6VOV)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 281 residues
Sequence: VYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNEGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2171
R free: 0.2675
Average B factor: 25.32
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 100mM Tris pH 8.5
Matthews coefficient: 2.18
Solvent content (%): 43.7
Ligand: 6-(6-aminopyrazin-2-yl)-N-{4-[4-(oxetan-3-yl)piperazin-1-yl]phenyl}imidazo[1,2-a]pyrazin-8-amine (R6D)
Ligand formula: C23 H25 N9 O
Ligand molecular weight: 443.504
Ligand SMILES: c1cc(ccc1Nc2c3nccn3cc(n2)c4cncc(n4)N)N5CCN(CC5)C6COC6
Ligand InChI: InChI=1S/C23H25N9O/c24-21-12-25-11-19(28-21)20-13-32-6-5-26-23(32)22(29-20)27-16-1-3-17(4-2-16)30-7-9-31(10-8-30)18-14-33-15-18/h1-6,11-13,18H,7-10,14-15H2,(H2,24,28)(H,27,29)
Release date: 2020-03-11
Crystal structure of human carbonic anhydrase II in complex with a heteroaryl-pyrazole carboxylic acid derivative. (PDB entry 6B4D)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.196
R work: 0.1389
R free: 0.156
Average B factor: 16.0164
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M sodium citrate, 50mM Tris HCl
Matthews coefficient: 2.13
Solvent content (%): 42.26
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: 2018-02-07
EGFR kinase domain mutant "TMLR" with compound 29 (PDB entry 5CAO)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2021
R free: 0.2305
Average B factor: 81.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 10000, ethlyene glycol
Matthews coefficient: 3.68
Solvent content (%): 66.6
Ligand: N~2~-[2-methyl-2-(methylsulfonyl)propyl]-N~4~-[2-methyl-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl]pyrimidine-2,4-diamine (4ZG)
Ligand formula: C19 H27 N7 O2 S
Ligand molecular weight: 417.528
Ligand SMILES: Cc1nc2cnc(cc2n1C(C)C)Nc3ccnc(n3)NCC(C)(C)S(=O)(=O)C
Ligand InChI: InChI=1S/C19H27N7O2S/c1-12(2)26-13(3)23-14-10-21-17(9-15(14)26)24-16-7-8-20-18(25-16)22-11-19(4,5)29(6,27)28/h7-10,12H,11H2,1-6H3,(H2,20,21,22,24,25)
Release date: 2015-10-28