satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human dihydroorotate dehydrogenase (DHODH) with compound 18T (PDB entry 5HQE)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 390 residues
Sequence: MGHHHHHHHHHHSSGHIDDDDKHMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.16022
R free: 0.18175
Average B factor: 21.41
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M acetate, 40mM C11DAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8 M ammonium sulfate
Matthews coefficient: 3.42
Solvent content (%): 64.04
Ligand: methyl (2Z)-cyano[3-(2-fluoro-4-methoxyphenyl)-4-oxo-1,3-thiazolidin-2-ylidene]acetate (64B)
Ligand formula: C14 H11 F N2 O4 S
Ligand molecular weight: 322.312
Ligand SMILES: COc1ccc(c(c1)F)N2C(=O)CSC2=C(C#N)C(=O)OC
Ligand InChI: InChI=1S/C14H11FN2O4S/c1-20-8-3-4-11(10(15)5-8)17-12(18)7-22-13(17)9(6-16)14(19)21-2/h3-5H,7H2,1-2H3/b13-9-
Release date: 2016-07-27
Crystal structure of human exonuclease 1 Exo1 (D173A) in complex with 5' recessed-end DNA (rVI) (PDB entry 5V08)
Macromolecule: DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*CP*GP*AP*CP*AP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 13 residues
Sequence: CGCTAGTCGACAT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.812
R work: 0.2147
R free: 0.2623
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000
Matthews coefficient: 2.66
Solvent content (%): 53.73
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: 2017-05-24
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQX)
Macromolecule: HEAT SHOCK 70 KDA PROTEIN 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 394 residues
Sequence: GPLGSMAKAAAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVALNPQNTVFDAKRLIGRKFGDPVVQSDMKHWPFQVINDGDKPKVQVSYKGETKAFYPEEISSMVLTKMKEIAEAYLGYPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDRTGKGERNVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVNHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQASLEIDSLFEGIDFYTSITRARFEELCSDLFRSTLEPVEKALRDAKLDKAQIHDLVLVGGSTRIPKVQKLLQDFFNGRDLNKSINPDEAVAYGAAVQAAILIKSTRAAAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.194
R free: 0.2273
Average B factor: 38.92
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 17-28% (W/V) PEG3350, 0.1 M HEPES PH 7.5, 2 MM MGCL2, 2 MM NAH2PO4 AND 5 MM ADENOSINE, THEN BACKSOAKED WITH 100 MM INHIBITOR (20% DMSO) FOR 16H AT 18 DEGREES C
Matthews coefficient: 2.32
Solvent content (%): 47.07
Ligand: (1R,2S,3R,5R)-3-((5-(benzyloxy)quinazolin-4-yl)amino)-5-(hydroxymethyl)cyclopentane-1,2-diol (KC7)
Ligand formula: C21 H23 N3 O4
Ligand molecular weight: 381.425
Ligand SMILES: c1ccc(cc1)COc2cccc3c2c(ncn3)NC4CC(C(C4O)O)CO
Ligand InChI: InChI=1S/C21H23N3O4/c25-10-14-9-16(20(27)19(14)26)24-21-18-15(22-12-23-21)7-4-8-17(18)28-11-13-5-2-1-3-6-13/h1-8,12,14,16,19-20,25-27H,9-11H2,(H,22,23,24)/t14-,16-,19-,20+/m1/s1
Release date: 2016-10-05
Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and 2-amino-4-oxo-4,7-dihydro-pyrrolo[2,3-d]pyrimidine-methyl-phenyl-D-glutamic acid (PDB entry 6OJU)
Macromolecule: Thymidylate synthase,Thymidylate synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.45
Sequence length: 290 residues
Sequence: MPVAGSELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.884
R work: 0.2131
R free: 0.2494
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 295.15
Crystal growth procedure: Well solution 0.1 M Na Acetate, 1.55 M Na formate
Seed Solution (diluted 50:1) 0.2 M MgCl2, 20 % PEG 3350 
Drop ratio 3:2:1 Enzyme mix/well solution/ seed solution
Matthews coefficient: 2.39
Solvent content (%): 48.5
Ligand: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (UMP)
Ligand formula: C9 H13 N2 O8 P
Ligand molecular weight: 308.182
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
Ligand InChI: InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
Release date: 2019-06-19
Crystal structure of EGFR 696-1022 T790M/C797S in complex with LS_2_40 (PDB entry 7ER2)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GAMGGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.662
R work: 0.1949
R free: 0.2417
Average B factor: 56.5444
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 38% PEG 300, 150 mM KCl, 0.1 M HEPES (pH 8.0)
Matthews coefficient: 3.46
Solvent content (%): 64.41
Ligand: 5-chloranyl-N2-[3-chloranyl-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]-N4-(2-dimethylphosphorylphenyl)pyrimidine-2,4-diamine (JAU)
Ligand formula: C28 H36 Cl2 N7 O P
Ligand molecular weight: 588.512
Ligand SMILES: CN1CCN(CC1)C2CCN(CC2)c3ccc(cc3Cl)Nc4ncc(c(n4)Nc5ccccc5P(=O)(C)C)Cl
Ligand InChI: InChI=1S/C28H36Cl2N7OP/c1-35-14-16-36(17-15-35)21-10-12-37(13-11-21)25-9-8-20(18-22(25)29)32-28-31-19-23(30)27(34-28)33-24-6-4-5-7-26(24)39(2,3)38/h4-9,18-19,21H,10-17H2,1-3H3,(H2,31,32,33,34)
Release date: 2022-04-20
Crystal Structure of human Pol alpha B-subunit in complex with C-terminal domain of catalytic subunit (PDB entry 4Y97)
Macromolecule: DNA polymerase alpha subunit B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 598 residues
Sequence: MSASAQQLAEELQIFGLDCEEALIEKLVELCVQYGQNEEGMVGELIAFCTSTHKVGLTSEILNSFEHEFLSKRLSKARHSTCKDSGHAGARDIVSIQELIEVEEEEEILLNSYTTPSKGSQKRAISTPETPLTKRSVSTRSPHQLLSPSSFSPSATPSQKYNSRSNRGEVVTSFGLAQGVSWSGRGGAGNISLKVLGCPEALTGSYKSMFQKLPDIREVLTCKIEELGSELKEHYKIEAFTPLLAPAQEPVTLLGQIGCDSNGKLNNKSVILEGDREHSSGAQIPVDLSELKEYSLFPGQVVIMEGINTTGRKLVATKLYEGVPLPFYQPTEEDADFEQSMVLVACGPYTTSDSITYDPLLDLIAVINHDRPDVCILFGPFLDAKHEQVENCLLTSPFEDIFKQCLRTIIEGTRSSGSHLVFVPSLRDVHHEPVYPQPPFSYSDLSREDKKQVQFVSEPCSLSINGVIFGLTSTDLLFHLGAEEISSSSGTSDRFSRILKHILTQRSYYPLYPPQEDMAIDYESFYVYAQLPVTPDVLIIPSELRYFVKDVLGCVCVNPGRLTKGQVGGTFARLYLRRPAADGAERQSPCIAVQVVRI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.218
R free: 0.257
Average B factor: 50.7
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 295
Crystal growth procedure: The diffraction quality crystals are growing in 2-3 weeks in 100 mM ammonium acetate, 50 mM Na citrate pH 5.6, 10 - 10.4% w/v PEG 4000, 2 mM TCEP and 50 mM guanidine HCl.
Matthews coefficient: 2.64
Solvent content (%): 53.42
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: 2015-04-15
uPA-BB2-28F (PDB entry 5ZAF)
Macromolecule: Urokinase-type plasminogen activator chain B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.205
R free: 0.236
Average B factor: 27.58
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400
Matthews coefficient: 2.18
Solvent content (%): 43.67
Ligand: 3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-(furan-3-yl)pyrazine-2-carboxamide (28I)
Ligand formula: C16 H21 N7 O2
Ligand molecular weight: 343.384
Ligand SMILES: c1cocc1c2c(nc(c(n2)C(=O)NC(=N)N)N)N3CCCCCC3
Ligand InChI: InChI=1S/C16H21N7O2/c17-13-12(15(24)22-16(18)19)20-11(10-5-8-25-9-10)14(21-13)23-6-3-1-2-4-7-23/h5,8-9H,1-4,6-7H2,(H2,17,21)(H4,18,19,22,24)
Release date: 2018-12-19
Crystal structure of human DNA polymerase eta incorporating dITP across dT (PDB entry 8FOG)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 432 residues
Sequence: MATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.2255
R free: 0.2896
Average B factor: 53.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, pH 6.5, 5 mM magnesium chloride, 18% PEG2000 MME
Matthews coefficient: 2.11
Solvent content (%): 41.73
Ligand: 2'-deoxyinosine 5'-triphosphate (Y43)
Ligand formula: C10 H15 N4 O13 P3
Ligand molecular weight: 492.166
Ligand SMILES: c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)NC=NC2=O
Ligand InChI: InChI=1S/C10H15N4O13P3/c15-5-1-7(14-4-13-8-9(14)11-3-12-10(8)16)25-6(5)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,15H,1-2H2,(H,20,21)(H,22,23)(H,11,12,16)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2023-05-03
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000211a (PDB entry 5QDJ)
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): 1.761
R work: 0.1818
R free: 0.2081
Average B factor: 35.1018
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: 3.32
Solvent content (%): 62.95
Ligand: N-(4-methyl-1,3-thiazol-2-yl)propanamide (JFP)
Ligand formula: C7 H10 N2 O S
Ligand molecular weight: 170.232
Ligand SMILES: CCC(=O)Nc1nc(cs1)C
Ligand InChI: InChI=1S/C7H10N2OS/c1-3-6(10)9-7-8-5(2)4-11-7/h4H,3H2,1-2H3,(H,8,9,10)
Release date: 2018-10-10
Structure of Human Vaccinia-related Kinase 1 (VRK1) bound to ACH471 (PDB entry 6VXU)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.184
R free: 0.203
Average B factor: 39.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 27.5% PEG3350; 300 mM LiSO4; 0.1 M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.5
Matthews coefficient: 2.58
Solvent content (%): 52.28
Ligand: (7R)-8-(cyclopropylmethyl)-2-[(3,5-difluoro-4-hydroxyphenyl)amino]-7-methyl-5-(prop-2-yn-1-yl)-7,8-dihydropteridin-6(5H)-one (RTJ)
Ligand formula: C20 H19 F2 N5 O2
Ligand molecular weight: 399.394
Ligand SMILES: CC1C(=O)N(c2cnc(nc2N1CC3CC3)Nc4cc(c(c(c4)F)O)F)CC#C
Ligand InChI: InChI=1S/C20H19F2N5O2/c1-3-6-26-16-9-23-20(24-13-7-14(21)17(28)15(22)8-13)25-18(16)27(10-12-4-5-12)11(2)19(26)29/h1,7-9,11-12,28H,4-6,10H2,2H3,(H,23,24,25)/t11-/m1/s1
Release date: 2021-03-03
JAK2 JH1 in complex with ruxolitinib (PDB entry 6VGL)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1803
R free: 0.2168
Average B factor: 44.5967
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris, pH 5.5, 0.2 M sodium chloride, 25% PEG3350
Matthews coefficient: 3.05
Solvent content (%): 59.72
Ligand: (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile (RXT)
Ligand formula: C17 H18 N6
Ligand molecular weight: 306.365
Ligand SMILES: c1c[nH]c2c1c(ncn2)c3cnn(c3)C(CC#N)C4CCCC4
Ligand InChI: InChI=1S/C17H18N6/c18-7-5-15(12-3-1-2-4-12)23-10-13(9-22-23)16-14-6-8-19-17(14)21-11-20-16/h6,8-12,15H,1-5H2,(H,19,20,21)/t15-/m1/s1
Release date: 2021-01-13
CLK1 bound with benzothiazole Tg003 (Cpd 2) (PDB entry 6YTE)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1805
R free: 0.2578
Average B factor: 23.657
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 277
Crystal growth procedure: 26% PEG 6k, 0.1M bicine
Matthews coefficient: 2.41
Solvent content (%): 48.94
Ligand: (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one (EAE)
Ligand formula: C13 H15 N O2 S
Ligand molecular weight: 249.329
Ligand SMILES: CCN1c2cc(ccc2SC1=CC(=O)C)OC
Ligand InChI: InChI=1S/C13H15NO2S/c1-4-14-11-8-10(16-3)5-6-12(11)17-13(14)7-9(2)15/h5-8H,4H2,1-3H3/b13-7-
Release date: 2020-07-15
XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM000893d (PDB entry 5S7J)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1577
R free: 0.1809
Average B factor: 19.228
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Matthews coefficient: 2.58
Solvent content (%): 52.3
Ligand: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine (LU8)
Ligand formula: C27 H32 N2 O3
Ligand molecular weight: 432.555
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H32N2O3/c1-18-23(21-8-6-19(7-9-21)20-10-12-29(2)13-11-20)16-28-17-24(18)22-14-25(30-3)27(32-5)26(15-22)31-4/h6-9,14-17,20H,10-13H2,1-5H3
Release date: 2021-06-23
Ternary complex crystal structure of DNA polymerase Beta with T:T mismatch at the primer terminus (PDB entry 5J2K)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2204
R free: 0.2837
Average B factor: 27.986
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.3
Solvent content (%): 46.59
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2016-10-26
Crystal structure of human tyrosinase related protein 1 in complex with kojic acid (PDB entry 5M8M)
Macromolecule: 5,6-dihydroxyindole-2-carboxylic acid oxidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.18
Sequence length: 446 residues
Sequence: QFPRQCATVEALRSGMCCPDLSPVSGPGTDRCGSSSGRGRCEAVTADSRPHSPQYPHDGRDDREVWPLRFFNRTCHCNGNFSGHNCGTCRPGWRGAACDQRVLIVRRNLLDLSKEEKNHFVRALDMAKRTTHPLFVIATRRSEEILGPDGNTPQFENISIYNYFVWTHYYSVKKTFLGVGQESFGEVDFSHEGPAFLTWHRYHLLRLEKDMQEMLQEPSFSLPYWNFATGKNVCDICTDDLMGSRSNFDSTLISPNSVFSQWRVVCDSLEDYDTLGTLCNSTEDGPIRRNPAGNVARPMVQRLPEPQDVAQCLEVGLFDTPPFYSNSTNSFRNTVEGYSDPTGKYDPAVRSLHNLAHLFLNGTGGQTHLSPNDPIFVLLHTFTDAVFDEWLRRYNADISTFPLENAPIGHNRQYNMVPFWPPVTNTEMFVTAPDNLGYTYEIQWPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1967
R free: 0.2494
Average B factor: 39.6045
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 0.1 M Tris (pH 7.0),
0.2 M NaCl and 30% (w/v) PEG 3000
Matthews coefficient: 3.03
Solvent content (%): 59.41
Ligand: 5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE (KOJ)
Ligand formula: C6 H6 O4
Ligand molecular weight: 142.109
Ligand SMILES: C1=C(OC=C(C1=O)O)CO
Ligand InChI: InChI=1S/C6H6O4/c7-2-4-1-5(8)6(9)3-10-4/h1,3,7,9H,2H2
Release date: 2017-07-12
Structure of human methionine aminopeptidase 2 with covalent spiroepoxytriazole inhibitor (-)-31b (PDB entry 5D6E)
Macromolecule: Methionine aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 371 residues
Sequence: GPKVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.11013
R free: 0.15559
Average B factor: 25.327
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.4
Crystallization temperature (K): 292
Crystal growth procedure: Na Citrate, Tert-butanol
Matthews coefficient: 2.71
Solvent content (%): 54.57
Ligand: (4R,7S)-7-hydroxy-1-(4-methoxybenzyl)-7-methyl-4,5,6,7-tetrahydro-1H-benzotriazol-4-yl propan-2-ylcarbamate (94A)
Ligand formula: C19 H26 N4 O4
Ligand molecular weight: 374.434
Ligand SMILES: CC(C)NC(=O)OC1CCC(c2c1nnn2Cc3ccc(cc3)OC)(C)O
Ligand InChI: InChI=1S/C19H26N4O4/c1-12(2)20-18(24)27-15-9-10-19(3,25)17-16(15)21-22-23(17)11-13-5-7-14(26-4)8-6-13/h5-8,12,15,25H,9-11H2,1-4H3,(H,20,24)/t15-,19+/m1/s1
Release date: 2016-01-13
KRAS-G13D-GDP in complex with Cpd5 (1-((S)-10-(6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl)-11-chloro-7-(((2S,4R)-4-fluoro-1-methylpyrrolidin-2-yl)methoxy)-3,4,13,13a-tetrahydropyrazino[2',1':3,4][1,4]oxazepino[5,6,7-de]quinazolin-2(1H)-yl)prop-2-en-1-one) (PDB entry 8UN3)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 168 residues
Sequence: STEYKLVVVGAGDVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.1623
R free: 0.1911
Average B factor: 38.7432
Crystallization method: EVAPORATION
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M Sodium Chloride, 0.1M Imidazole pH8.0, 0.4M Sodium di-hydrogen Phosphate, 1.6M Di-potassium Hydrogen Phosphate
Matthews coefficient: 3.01
Solvent content (%): 59.17
Ligand: 1-[(5M,8aS,13R)-5-[6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl]-6-chloro-2-{[(2S,4R)-4-fluoro-1-methylpyrrolidin-2-yl]methoxy}-8a,9,11,12-tetrahydropyrazino[2',1':3,4][1,4]oxazepino[5,6,7-de]quinazolin-10(8H)-yl]prop-2-en-1-one (XOI)
Ligand formula: C29 H30 Cl F4 N7 O3
Ligand molecular weight: 636.04
Ligand SMILES: Cc1cc(nc(c1C(F)(F)F)c2cc3c4c(c2Cl)OCC5CN(CCN5c4nc(n3)OCC6CC(CN6C)F)C(=O)C=C)N
Ligand InChI: InChI=1S/C29H30ClF4N7O3/c1-4-21(42)40-5-6-41-17(11-40)13-43-26-22-19(36-28(38-27(22)41)44-12-16-8-15(31)10-39(16)3)9-18(24(26)30)25-23(29(32,33)34)14(2)7-20(35)37-25/h4,7,9,15-17H,1,5-6,8,10-13H2,2-3H3,(H2,35,37)/t15-,16+,17+/m1/s1
Release date: 2023-12-20