satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human polymerase eta with incoming dAMPnPP nucleotide opposite urea lesion (PDB entry 8UJT)
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): 2.31
R work: 0.1778
R free: 0.2434
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH 6.0, 5mM magnesium chloride, 22% PEG MME 2000
Matthews coefficient: 2.13
Solvent content (%): 42.26
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine (DZ4)
Ligand formula: C10 H17 N6 O11 P3
Ligand molecular weight: 490.197
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
Release date: 2024-03-20
THE STRUCTURE OF JNK3 IN COMPLEX WITH AN IMIDAZOLE-PYRIMIDINE INHIBITOR (PDB entry 4Z9L)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 364 residues
Sequence: MASKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1997
R free: 0.2258
Average B factor: 29.49
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: PEG MME 550, ETHYLENE GLYCOL,  HEPES
Matthews coefficient: 2.3
Solvent content (%): 46.5
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2015-05-06
Crystal structure of human T1061E PI3Kalpha in complex with its regulatory subunit and the inhibitor GDC-0077 (Inavolisib) (PDB entry 8AM0)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.137
Sequence length: 1068 residues
Sequence: MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKMDWIFHEIKQHALN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.818
R work: 0.2854
R free: 0.3
Average B factor: 69.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.1
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M Bis-Tris-Propane pH 8.10, 0.20 M Na 3 -citrate, 10.00 %(w/v) PEG 3350
Matthews coefficient: 2.29
Solvent content (%): 46.37
Ligand: (2R)-2-[[2-[(4S)-4-[bis(fluoranyl)methyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl]amino]propanamide (MWF)
Ligand formula: C18 H19 F2 N5 O4
Ligand molecular weight: 407.371
Ligand SMILES: CC(C(=O)N)Nc1ccc-2c(c1)OCCn3c2nc(c3)N4C(COC4=O)C(F)F
Ligand InChI: InChI=1S/C18H19F2N5O4/c1-9(16(21)26)22-10-2-3-11-13(6-10)28-5-4-24-7-14(23-17(11)24)25-12(15(19)20)8-29-18(25)27/h2-3,6-7,9,12,15,22H,4-5,8H2,1H3,(H2,21,26)/t9-,12+/m1/s1
Release date: 2023-12-13
Crystal structure of FGFR4(V550L) kinase domain with 7v (PDB entry 7WCW)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: LLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGAFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVILECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.317
R work: 0.1763
R free: 0.2214
Average B factor: 31.5034
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 4.5), 0.2 M Li2SO4, 16-19 % PEG3350
Matthews coefficient: 2.24
Solvent content (%): 45.05
Ligand: ~{N}-[2-[[5-[(1~{R})-1-[3,5-bis(chloranyl)pyridin-4-yl]ethoxy]-1~{H}-indazol-3-yl]amino]-3-fluoranyl-5-(4-morpholin-4-ylpiperidin-1-yl)phenyl]propanamide (90F)
Ligand formula: C32 H36 Cl2 F N7 O3
Ligand molecular weight: 656.578
Ligand SMILES: CCC(=O)Nc1cc(cc(c1Nc2c3cc(ccc3[nH]n2)OC(C)c4c(cncc4Cl)Cl)F)N5CCC(CC5)N6CCOCC6
Ligand InChI: InChI=1S/C32H36Cl2FN7O3/c1-3-29(43)37-28-15-21(41-8-6-20(7-9-41)42-10-12-44-13-11-42)14-26(35)31(28)38-32-23-16-22(4-5-27(23)39-40-32)45-19(2)30-24(33)17-36-18-25(30)34/h4-5,14-20H,3,6-13H2,1-2H3,(H,37,43)(H2,38,39,40)/t19-/m1/s1
Release date: 2022-03-30
Complement factor B in complex with (-)-4-(1-((5,7-Dimethyl-1H-indol-4-yl)methyl)piperidin-2-yl)benzoic acid (PDB entry 6T8W)
Macromolecule: Complement factor B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.47
Sequence length: 291 residues
Sequence: SLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1975
R free: 0.2383
Average B factor: 28.47
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG3350, 0.1M BIS-TRIS PH 6.5, 0.2M        
AMMONIUM SULFATE, 0.1 MM ZNCL2, 1 mM inhibitor
Matthews coefficient: 2.47
Solvent content (%): 50.14
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2020-03-04
Crystal structure of TrkA in complex with PF-05247452 (PDB entry 5JFW)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 308 residues
Sequence: MHHHHHHLVPRGSVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.1786
R free: 0.2093
Average B factor: 25.82
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: protein was concentrated to 10mg/ml. Crystals of complexes were grown using the hanging drop vapour diffusion method from 0.1M HEPES pH7.5, 0.1M MgCl2 and 10% EtOH at 4C
Matthews coefficient: 2.94
Solvent content (%): 62.16
Ligand: 2-(4-cyanophenyl)-N-{5-[7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonyl]pyridin-3-yl}acetamide (6K2)
Ligand formula: C24 H20 N6 O2
Ligand molecular weight: 424.455
Ligand SMILES: CC(C)n1cc(c2c1ncnc2)C(=O)c3cc(cnc3)NC(=O)Cc4ccc(cc4)C#N
Ligand InChI: InChI=1S/C24H20N6O2/c1-15(2)30-13-21(20-12-27-14-28-24(20)30)23(32)18-8-19(11-26-10-18)29-22(31)7-16-3-5-17(9-25)6-4-16/h3-6,8,10-15H,7H2,1-2H3,(H,29,31)
Release date: 2017-03-01
Structure of the enzyme-product complex resulting from TDG action on a G/hmU mismatch (PDB entry 4XEG)
Macromolecule: G/T mismatch-specific thymine DNA glycosylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.29
Sequence length: 204 residues
Sequence: GSHMASFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.1882
R free: 0.2315
Average B factor: 38.544
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 20% (w/v) PEG 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 6.0
Matthews coefficient: 2.47
Solvent content (%): 50.27
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: 2015-09-09
Crystal structure of COT kinase domain in complex with 5-(2-amino-5-(quinolin-3-yl)pyridin-3-yl)-1,3,4-oxadiazole-2(3H)-thione (PDB entry 4Y83)
Macromolecule: Mitogen-activated protein kinase kinase kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 332 residues
Sequence: GPSGQEVPWLSSVRYGTVEDLLAFANHISNTAKHFYGQRPQESGILLNMVITPQNGRYQIDSDVLLIPWKLTYRNIGSDFIPRGAFGKVYLAQDIKTKKRMACKLIPVDQFKPSDVEIQACFRHENIAELYGAVLWGETVHLFMEAGEGGSVLEKLESCGPMREFEIIWVTKHVLKGLDFLHSKKVIHHDIKPSNIVFMSTKAVLVDFGLSVQMTEDVYFPKDLRGTEIYMSPEVILCRGHSTKADIYSLGATLIHMQTGTPPWVKRYPRSAYPSYLYIIHKQAPPLEDIADDCSPGMRELIEASLERNPNHRPRAADLLKHEALNPPREDQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.89
R work: 0.2017
R free: 0.2395
Average B factor: 61.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 298
Crystal growth procedure: Reservoir solution: 8% (w/v) PEG4000, 12% (v/v) ethylene glycol, 7% (v/v) iso-propanol
Matthews coefficient: 2.88
Solvent content (%): 57.27
Ligand: 5-[2-amino-5-(quinolin-3-yl)pyridin-3-yl]-1,3,4-oxadiazole-2(3H)-thione (49B)
Ligand formula: C16 H11 N5 O S
Ligand molecular weight: 321.356
Ligand SMILES: c1ccc2c(c1)cc(cn2)c3cc(c(nc3)N)C4=NNC(=S)O4
Ligand InChI: InChI=1S/C16H11N5OS/c17-14-12(15-20-21-16(23)22-15)6-11(8-19-14)10-5-9-3-1-2-4-13(9)18-7-10/h1-8H,(H2,17,19)(H,21,23)
Release date: 2015-05-06
Crystal Structure of Human DHFR complexed with NADP and N10formyltetrahydrofolate (PDB entry 6DAV)
Macromolecule: Dihydrofolate reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.3
Sequence length: 187 residues
Sequence: MVGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1652
R free: 0.2044
Average B factor: 32.178
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 290
Crystal growth procedure: Wizard 3/4 H10 (296175h10): 100 mM Tris base/ Hydrochloric acid pH 8.5, 30% (w/v) PEG3350, 30% (v/v) 2-propanol, protein conc. 28.74 mg/mL, protein batch ID XP819, 10 mM NADP, 3.75 mM BSI108214, seeded from 293949g10, cryoprotected with 20% eg, puck izs6-6
Matthews coefficient: 2.24
Solvent content (%): 45
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/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/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2018-05-16
Crystal Structure of the Activated FGF Receptor 2 (FGFR2) Kinase Domain in complex with the cSH2 domain of Phospholipase C gamma (PLCgamma) (PDB entry 5EG3)
Macromolecule: Fibroblast growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 334 residues
Sequence: MGSSHHHHHHSQDPMLAGVSEFELPEDPKWEFPRDKLTLGKPLGEGAFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVAYASKGNLREYLRARRPPGMELSPDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDFFKETTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLTTNEEYLDLSQPLEQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.606
R work: 0.1854
R free: 0.2373
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 25 mM HEPES (pH 7.5), PEG20000 (12% 18%) and 2% (w/v) Benzamidine hydrochloride
Matthews coefficient: 2.59
Solvent content (%): 52.46
Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER (ACP)
Ligand formula: C11 H18 N5 O12 P3
Ligand molecular weight: 505.208
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
Release date: 2016-02-03
Crystal structure of human UCHL3 in complex with Farrerol (PDB entry 7YV4)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase isozyme L3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 230 residues
Sequence: MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.1789
R free: 0.2063
Average B factor: 27.1534
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289.15
Crystal growth procedure: 1.4M Sodium Citrate tribasic dihydrate, 0.1M HEPES Sodium pH 7.0
Matthews coefficient: 2.21
Solvent content (%): 44.39
Ligand: (2~{S})-2-(4-hydroxyphenyl)-6,8-dimethyl-5,7-bis(oxidanyl)-2,3-dihydrochromen-4-one (JXY)
Ligand formula: C17 H16 O5
Ligand molecular weight: 300.306
Ligand SMILES: Cc1c(c(c2c(c1O)C(=O)CC(O2)c3ccc(cc3)O)C)O
Ligand InChI: InChI=1S/C17H16O5/c1-8-15(20)9(2)17-14(16(8)21)12(19)7-13(22-17)10-3-5-11(18)6-4-10/h3-6,13,18,20-21H,7H2,1-2H3/t13-/m0/s1
Release date: 2023-04-19
Crystal structure of human tyrosine-protein kinase Fes/Fps in complex with compound 4 (PDB entry 6JMF)
Macromolecule: Tyrosine-protein kinase Fes/Fps
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 375 residues
Sequence: GPEVQKPLHEQLWYHGAIPRAEVAELLVHSGDFLVRESQGKQEYVLSVLWDGLPRHFIIQSLDNLYRLEGEGFPSIPLLIDHLLSTQQPLTKKSGVVLHRAVPKDKWVLNHEDLVLGEQIGRGNFGEVFSGRLRADNTLVAVKSCRETLPPDLKAKFLQEARILKQYSHPNIVRLIGVCTQKQPIYIVMELVQGGDFLTFLRTEGARLRVKTLLQMVGDAAAGMEYLESKCCIHRDLAARNCLVTEKNVLKISDFGMSREEADGVYAASGGLRQVPVKWTAPEALNYGRYSSESDVWSFGILLWETFSLGASPYPNLSNQQTREFVEKGGRLPCPELCPDAVFRLMEQCWAYEPGQRPSFSTIYQELQSIRKRHR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.19737
R free: 0.24082
Average B factor: 26.576
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M BisTrisPropane, 0.2 M Sodium Salfate, 15% PEG 3350, 10% Ethylene glycol
Matthews coefficient: 2.68
Solvent content (%): 54.03
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: 2019-06-12
Co-structure of BTK kinase domain with L-005085737 inhibitor (PDB entry 6X3N)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2136
R free: 0.2417
Average B factor: 46.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Bis-TRIS pH 6.5, 0.1M NaCl, 15% w/v PEG 20K 5mM TCEP Cl, 4mM (S)-4-(8-amino-3-(1-(4-(dimethylamino)butanoyl)pyrrolidin-2-yl)imidazo[1,5-a]pyrazin-1-yl)-N-(thiazol-2-yl)benzamide
Matthews coefficient: 2.29
Solvent content (%): 46.24
Ligand: 4-{8-amino-3-[(6R,8aS)-3-oxohexahydro-3H-[1,3]oxazolo[3,4-a]pyridin-6-yl]imidazo[1,5-a]pyrazin-1-yl}-N-[4-(trifluoromethyl)pyridin-2-yl]benzamide (ULV)
Ligand formula: C26 H22 F3 N7 O3
Ligand molecular weight: 537.493
Ligand SMILES: c1cc(ccc1c2c3c(nccn3c(n2)C4CCC5COC(=O)N5C4)N)C(=O)Nc6cc(ccn6)C(F)(F)F
Ligand InChI: InChI=1S/C26H22F3N7O3/c27-26(28,29)17-7-8-31-19(11-17)33-24(37)15-3-1-14(2-4-15)20-21-22(30)32-9-10-35(21)23(34-20)16-5-6-18-13-39-25(38)36(18)12-16/h1-4,7-11,16,18H,5-6,12-13H2,(H2,30,32)(H,31,33,37)/t16-,18+/m1/s1
Release date: 2020-07-22
Ternary complex crystal structure of DNA polymerase Beta with R-isomer of beta-gamma-CHF-dCTP (PDB entry 6BEL)
Macromolecule: Template Strand
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACGTCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.898
R work: 0.1678
R free: 0.2015
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.28
Solvent content (%): 46.16
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: 2018-10-31
DNA Polymerase Mu, dGTP:Ct Product State Ternary Complex, 10 mM Mg2+ (30min) (PDB entry 7KSX)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1633
R free: 0.186
Average B factor: 28.8059
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.5
Solvent content (%): 50.89
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: 2021-12-01
TRK-A IN COMPLEX WITH LIGAND 6 (PDB entry 6NSS)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.18063
R free: 0.21805
Average B factor: 32.164
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.10M KH2PO4/ 0.10M NaH2PO4/ 0.1M MES/NaOH pH = 6.00 and 1.9M NaCl (cryo: 25% glycerol in reservoir), or 18% (w/v) PEG 3350, 0.2M CaCl2, 0.10M, MES pH = 6.50 (cryo: direct).
Matthews coefficient: 2.54
Solvent content (%): 51.61
Ligand: N-(8-methyl-2-phenylimidazo[1,2-a]pyrazin-3-yl)-2-(10H-phenoxazin-10-yl)acetamide (L0M)
Ligand formula: C27 H21 N5 O2
Ligand molecular weight: 447.488
Ligand SMILES: Cc1c2nc(c(n2ccn1)NC(=O)CN3c4ccccc4Oc5c3cccc5)c6ccccc6
Ligand InChI: InChI=1S/C27H21N5O2/c1-18-26-30-25(19-9-3-2-4-10-19)27(31(26)16-15-28-18)29-24(33)17-32-20-11-5-7-13-22(20)34-23-14-8-6-12-21(23)32/h2-16H,17H2,1H3,(H,29,33)
Release date: 2019-05-22