satarupa22/MacromolecularLigandDB huggingface dataset:
human dihydrofolate reductase complex with NADPH and 5-methyl-6-(phenylthio-4'trifluoromethyl)thieno[2,3-d]pyrimidine-2,4-diamine (PDB entry 5HPB)
Macromolecule: Dihydrofolate reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.3
Sequence length: 186 residues
Sequence: VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.2364
R free: 0.29278
Average B factor: 36.319
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 287
Crystal growth procedure: 100 mM KPO4, 30% sat AmSO4, 3% v/vEtOH
Matthews coefficient: 2.55
Solvent content (%): 51.73
Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NDP)
Ligand formula: C21 H30 N7 O17 P3
Ligand molecular weight: 745.421
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
Ligand InChI: InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2017-01-25
Crystal structure of JAK2 JH2 (pseudokinase domain) in complex with CDK2-IV (PDB entry 8EX0)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1749
R free: 0.2276
Average B factor: 33.69
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 277
Crystal growth procedure: CHES, PEG 3000
Matthews coefficient: 2.33
Solvent content (%): 47.12
Ligand: 4-{[6-(cyclohexylmethoxy)-7H-purin-2-yl]amino}-N,N-diethylbenzamide (AQG)
Ligand formula: C23 H30 N6 O2
Ligand molecular weight: 422.523
Ligand SMILES: CCN(CC)C(=O)c1ccc(cc1)Nc2nc3c(c(n2)OCC4CCCCC4)[nH]cn3
Ligand InChI: InChI=1S/C23H30N6O2/c1-3-29(4-2)22(30)17-10-12-18(13-11-17)26-23-27-20-19(24-15-25-20)21(28-23)31-14-16-8-6-5-7-9-16/h10-13,15-16H,3-9,14H2,1-2H3,(H2,24,25,26,27,28)
Release date: 2023-02-01
Crystal structure of human chitotriosidase-1 (hChit1) catalytic domain in complex with compound 2-8-14 (PDB entry 6JJR)
Macromolecule: Chitotriosidase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.14
Sequence length: 381 residues
Sequence: AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEESGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQELSLPYLPSGTPEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.834
R work: 0.1672
R free: 0.194
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 277
Crystal growth procedure: 25% (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate (PST) pH 7.2
Matthews coefficient: 2.24
Solvent content (%): 45.21
Ligand: 6-azanyl-2-oxidanylidene-N-[(1S)-1-phenylethyl]-7-(phenylmethyl)-1$l^{4},9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-1(14),3(8),4,6,10,12-hexaene-5-carboxamide (BU0)
Ligand formula: C27 H25 N5 O2
Ligand molecular weight: 451.52
Ligand SMILES: CC(c1ccccc1)NC(=O)c2cc3c([n+](c2N)Cc4ccccc4)Nc5cccc[n+]5C3=O
Ligand InChI: InChI=1S/C27H23N5O2/c1-18(20-12-6-3-7-13-20)29-26(33)21-16-22-25(30-23-14-8-9-15-31(23)27(22)34)32(24(21)28)17-19-10-4-2-5-11-19/h2-16,18,28H,17H2,1H3,(H,29,33)/p+2/t18-/m0/s1
Release date: 2020-02-19
Human DNMT3B PWWP domain in complex with 6-dipropylamino-1-hexanol (PDB entry 5NRV)
Macromolecule: DNA (cytosine-5)-methyltransferase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 150 residues
Sequence: EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.075
R work: 0.2071
R free: 0.2435
Average B factor: 38.52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES,0.2 M Li2SO4, 23-33% PEG 3350
Matthews coefficient: 3.63
Solvent content (%): 66.12
Ligand: 6-dipropylamino-1-hexanol (96K)
Ligand formula: C12 H27 N O
Ligand molecular weight: 201.349
Ligand SMILES: CCCN(CCC)CCCCCCO
Ligand InChI: InChI=1S/C12H27NO/c1-3-9-13(10-4-2)11-7-5-6-8-12-14/h14H,3-12H2,1-2H3
Release date: 2018-06-13
Aspartyl/Asparaginyl beta-hydroxylase (AspH) oxygenase and TPR domains in complex with manganese, 5-fluoropyridine-2,4-dicarboxylic acid, and factor X substrate peptide fragment (39mer-4Ser) (PDB entry 7BMJ)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.6
Sequence length: 39 residues
Sequence: DGDQSETSPSQNQGKCKDGLGEYTCTSLEGFEGKNSELF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.2208
R free: 0.2512
Average B factor: 62.53
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 200 mM sodium nitrate, 20% w/v PEG 3350, 1 mM manganese chloride, 18 mg/ml protein
Matthews coefficient: 2.63
Solvent content (%): 53.3
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: 2021-06-02
Crystal structure of human KRAS G12V mutant in complex with GDP (PDB entry 5UQW)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 189 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.11666
R free: 0.15272
Average B factor: 16.818
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Bis-Tris, 25% w/v PEG3350, pH 6.5
Matthews coefficient: 2
Solvent content (%): 38.44
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2017-03-22
LSD1-CoREST in complex with T108, short soaking (PDB entry 8FJ4)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 871 residues
Sequence: GSSHHHHHHSSGLVPRGSHMLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTPRKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEYREMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQATPGVPAQQSPSM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.76
R work: 0.224
R free: 0.2477
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Matthews coefficient: 5.54
Solvent content (%): 77.8
Ligand: 3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-phenylbenzamide (XZU)
Ligand formula: C20 H22 N2 O
Ligand molecular weight: 306.401
Ligand SMILES: c1ccc(cc1)NC(=O)c2cccc(c2)C3CC3NC4CCC4
Ligand InChI: InChI=1S/C20H22N2O/c23-20(22-17-8-2-1-3-9-17)15-7-4-6-14(12-15)18-13-19(18)21-16-10-5-11-16/h1-4,6-9,12,16,18-19,21H,5,10-11,13H2,(H,22,23)/t18-,19+/m1/s1
Release date: 2024-06-26
Structure of CO2 released apo-form of human carbonic anhydrase II with 10 min warming (PDB entry 5DSR)
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): 1.3
R work: 0.1225
R free: 0.15274
Average B factor: 13.589
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate
100 mM TrisHCl pH 7.8
Matthews coefficient: 2.09
Solvent content (%): 41.02
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: 2016-05-04
Crystal Structures of PIM1 in Complex with Macrocyclic Compound H3 (PDB entry 7XSV)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 289 residues
Sequence: GPHMKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.66
R work: 0.1927
R free: 0.2332
Average B factor: 69.231
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 0.4M POTASSIUM SODIUM TARTRATE
Matthews coefficient: 3.24
Solvent content (%): 61.99
Ligand: 8-Methyl-2,5,20-trioxa-8,13,17-triazatetracyclo[11.10.2.014,19.021,25]pentacosa-1(24),14(19),15,17,21(25),22-hexaene (I4M)
Ligand formula: C20 H25 N3 O3
Ligand molecular weight: 355.431
Ligand SMILES: CN1CCCCN2c3ccncc3Oc4c2cc(cc4)OCCOCC1
Ligand InChI: InChI=1S/C20H25N3O3/c1-22-8-2-3-9-23-17-6-7-21-15-20(17)26-19-5-4-16(14-18(19)23)25-13-12-24-11-10-22/h4-7,14-15H,2-3,8-13H2,1H3
Release date: 2022-07-13
Crystal structure of human KDM4A in complex with compound 19d (PDB entry 6H4W)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.81
R work: 0.218
R free: 0.266
Average B factor: 53.96
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Matthews coefficient: 2.45
Solvent content (%): 49.83
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2019-06-12
MbC/SHP1-C-SH2 complex (PDB entry 6SM5)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 120 residues
Sequence: GSLNCSDPTSERWYHGHMSGGQAETLLQAKGEPWTFLVRESLSQPGDFVLSVLSDQPKAGPGSPLRVTHIKVMCEGGRYTVGGLETFDSLTDLVEHFKKTGIEEASGAFVYLRQPYYKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.219127249237
R free: 0.276452644706
Average B factor: 32.9141762171
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M sodium citrate tribasic, 0.1 M bistros propane 8.4 and 20 % PEG 3350
Matthews coefficient: 2.62
Solvent content (%): 53.1
Release date: 2021-01-13
Co-crystal structure of human PRMT9 in complex with MT221 inhibitor (PDB entry 7T39)
Macromolecule: Protein arginine N-methyltransferase 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.320
Sequence length: 720 residues
Sequence: GAVKLNPDFSDAKENFYRVANWLVERWHFIMLNDTKRNTIYNAAIQKAVCLGSKSVLDIGAGTGILSMFAKKAGAHSVYACELSKTMYELACDVVAANKMEAGIKLLHTKSLDIEIPKHIPERVSLVVTETVDAGLFGEGIVESLIHAWEHLLLQPKTKGESANCEKYGKVIPASAVIFGMAVECAEIRRHHRVGIKDIAGIHLPTNVKFQSPAYSSVDTEETIEPYTTEKMSRVPGGYLALTECFEIMTVDFNNLQELKSLATKKPDKIGIPVIKEGILDAIMVWFVLQLDDEHSLSTSPSEETCWEQAVYPVQDLADYWIKPGDHVMMEVSCQDCYLRIQSISVLGLECEMDVAKSFTQNKDLLSLGNEAELCSALANLQTSKPDAVEQTCILESTEIALLNNIPYHEGFKMAMSKVLSSLTPEKLYQTMDTHCQNEMSSGTGQSNTVQNILEPFYVLDVSEGFSVLPVIAGTLGQVKPYSSVEKDQHRIALDLISEANHFPKETLEFWLRHVEDESAMLQRPKSDKLWSIIILDVIEPSGLIQQEIMEKAAISRCLLQSGGKIFPQYVLMFGLLVESQTLLEENAVQGTERTLGLNIAPFINQFQVPIRVFLDLSSLPCIPLSKPVELLRLDLMTPYLNTSNREVKVYVCKSGRLTAIPFWYHMYLDEEIRLDTSSEASHWKQAAVVLDNPIQVEMGEELVLSIQHHKSNVSITVKQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.81
R work: 0.228
R free: 0.2686
Average B factor: 54.646
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 291
Crystal growth procedure: 25%(w/v) PEG3350, 0.2M Ammonium Acetate, 0.1M Bis-Tris pH5.5
Matthews coefficient: 2.15
Solvent content (%): 42.78
Ligand: 7-[5-S-(4-{[(2-ethylpyridin-3-yl)methyl]amino}butyl)-5-thio-beta-D-ribofuranosyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine (EJB)
Ligand formula: C23 H32 N6 O3 S
Ligand molecular weight: 472.604
Ligand SMILES: CCc1c(cccn1)CNCCCCSCC2C(C(C(O2)n3ccc4c3ncnc4N)O)O
Ligand InChI: InChI=1S/C23H32N6O3S/c1-2-17-15(6-5-9-26-17)12-25-8-3-4-11-33-13-18-19(30)20(31)23(32-18)29-10-7-16-21(24)27-14-28-22(16)29/h5-7,9-10,14,18-20,23,25,30-31H,2-4,8,11-13H2,1H3,(H2,24,27,28)/t18-,19-,20-,23-/m1/s1
Release date: 2021-12-22
Crystal structure of the human METTL3-METTL14 complex with compound UOZ016 (PDB entry 7NHV)
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): 1.91
R work: 0.1956
R free: 0.2119
Average B factor: 38.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.13
Solvent content (%): 42.37
Ligand: (R)-N-((1-(6-(benzylamino)pyrimidin-4-yl)-3-hydroxypiperidin-3-yl)methyl)-4-((4,4-dimethylpiperidin-1-yl)methyl)benzamide (UE5)
Ligand formula: C32 H42 N6 O2
Ligand molecular weight: 542.715
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(cc2)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NCc5ccccc5)O)C
Ligand InChI: InChI=1S/C32H42N6O2/c1-31(2)14-17-37(18-15-31)21-26-9-11-27(12-10-26)30(39)34-22-32(40)13-6-16-38(23-32)29-19-28(35-24-36-29)33-20-25-7-4-3-5-8-25/h3-5,7-12,19,24,40H,6,13-18,20-23H2,1-2H3,(H,34,39)(H,33,35,36)/t32-/m1/s1
Release date: 2021-10-20
Soluble epoxide hydrolase in complex with Epoxykinin (PDB entry 8QZD)
Macromolecule: Bifunctional epoxide hydrolase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.10
Sequence length: 367 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARNPPVVSKMLLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.16279
R free: 0.18041
Average B factor: 18.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG Smear High, 0.1M PIPES pH 7.0, 0.1M magnesium formate, 0.1M rubidium chloride
Matthews coefficient: 1.96
Solvent content (%): 37.18
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: 2024-02-28
KRAS4b A146T 1-185 bound to GDP (PDB entry 8EDY)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSTKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.18
R work: 0.1617
R free: 0.1718
Average B factor: 17.08
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 22% PEG3350, 200 mM lithium citrate, 10 uM GDP, 1 mM magnesium chloride, 2 mM DTT, 20 mM sodium chloride, 10 mM Tris-HCl, pH 8
Matthews coefficient: 2.49
Solvent content (%): 50.69
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: 2023-09-20
Crystal Structure of double mutant Y115E Y117E human Glutaminyl Cyclase (PDB entry 4YU9)
Macromolecule: Glutaminyl-peptide cyclotransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.5
Sequence length: 329 residues
Sequence: ASAWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPEGERSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.21079
R free: 0.2542
Average B factor: 13.992
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 281
Crystal growth procedure: 0.1 M MES pH 6.5, 1.6 M Ammonium Sulfate
Matthews coefficient: 2.75
Solvent content (%): 55.24
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: 2015-08-05
Structure of Mouse Importin alpha NEIL3 NLS Peptide Complex (PDB entry 7TMY)
Macromolecule: Importin subunit alpha-1
Type: Protein, polypeptide(L)
Source organism: Mus musculus
Sequence length: 460 residues
Sequence: NQGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFESAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSAFRDLVIKHGAIDPLLALLAVPDLSTLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTDGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTNIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCGIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQRHENESVYKASLNLIEKYFSVEEEEDQNVVPETTSEGFAFQVQDGAPGTFNF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.1857
R free: 0.2168
Average B factor: 56.068
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: sodium citrate buffer (pH 6.0), sodium citrate and DTT
Matthews coefficient: 3.46
Solvent content (%): 64.42
Release date: 2023-08-02
Crystal structure of the catalytic domain of human JARID1B in complex with 2,5-dichloro-N-(pyridin-3-yl)thiophene-3-carboxamide (N08137b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) (PDB entry 5FZ0)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.42
R work: 0.1918
R free: 0.2332
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.19
Solvent content (%): 43.84
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: 2016-04-06