satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 1l (PDB entry 5NK3)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.586
R work: 0.1932
R free: 0.2278
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD/PEG1000/PEG3350 (MD), 0.3 M Amino Acids Mix (MD), 0.1 M MES pH6.0
Matthews coefficient: 1.85
Solvent content (%): 33.34
Ligand: ~{N}-(2-chloranyl-6-methyl-phenyl)-2-[[3-[[(3~{S})-pyrrolidin-3-yl]carbamoyl]phenyl]amino]-1,3-thiazole-5-carboxamide (92Q)
Ligand formula: C22 H22 Cl N5 O2 S
Ligand molecular weight: 455.96
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cccc(c3)C(=O)NC4CCNC4)Cl
Ligand InChI: InChI=1S/C22H22ClN5O2S/c1-13-4-2-7-17(23)19(13)28-21(30)18-12-25-22(31-18)27-15-6-3-5-14(10-15)20(29)26-16-8-9-24-11-16/h2-7,10,12,16,24H,8-9,11H2,1H3,(H,25,27)(H,26,29)(H,28,30)/t16-/m0/s1
Release date: 2017-06-07
Crystal Structure of Adaptor Protein 2 Associated Kinase 1 (AAK1) in Complex with LKB1 (AAK1 Dual Inhibitor) (PDB entry 5L4Q)
Macromolecule: AP2-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 346 residues
Sequence: TSGLGSGYIGRVFGIGRQQVTVDEVLAEGGFAIVFLVRTSNGMKCALKRMFVNNEHDLQVCKREIQIMRDLSGHKNIVGYIDSSINNVSSGDVWEVLILMDFCRGGQVVNLMNQRLQTGFTENEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLHDRGHYVLCDFGSATNKFQNPQTEGVNAVEDEIKKYTTLSYRAPEMVNLYSGKIITTKADIWALGCLLYKLCYFTLPFGESQVAICDGNFTIPDNSRYSQDMHCLIRYMLEPDPDKRPDIYQVSYFSFKLLKKECPIPNVQNSPIPAKLPEPVKASEAAAKKTQPKARLTDPIPTTETSIAAENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.2071
R free: 0.2265
Average B factor: 44.2379
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5, 26% PEG3350
Matthews coefficient: 1.83
Solvent content (%): 32.81
Ligand: ~{N}-[5-(4-cyanophenyl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]pyridine-3-carboxamide (LKB)
Ligand formula: C20 H13 N5 O
Ligand molecular weight: 339.35
Ligand SMILES: c1cc(cnc1)C(=O)Nc2c[nH]c3c2cc(cn3)c4ccc(cc4)C#N
Ligand InChI: InChI=1S/C20H13N5O/c21-9-13-3-5-14(6-4-13)16-8-17-18(12-24-19(17)23-11-16)25-20(26)15-2-1-7-22-10-15/h1-8,10-12H,(H,23,24)(H,25,26)
Release date: 2016-06-08
XChem group deposition -- Crystal Structure of human ACVR1 in complex with XS035133b (PDB entry 5S77)
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: 0.1646
R free: 0.1851
Average B factor: 18.008
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: 2.6
Solvent content (%): 52.6
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
Crystal structure of human Sirt3 in complex with an inhibiting HIV1 Tat-37-59 peptide (PDB entry 8CCZ)
Macromolecule: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 282 residues
Sequence: SDKGKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLDGPDK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2269
R free: 0.2763
Average B factor: 38.87
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM Tat-37-59 in 10% (v/v) DMSO for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM CHES, pH 9.0, 20% (w/v) PEG 8000 as reservoir solution.
Matthews coefficient: 2.38
Solvent content (%): 48.32
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: 2023-05-10
Human Sirt6 in complex with activator UBCS58 (PDB entry 5MFP)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1572
R free: 0.18493
Average B factor: 33.575
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.59
Solvent content (%): 52.45
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2016-12-28
EGFR(T790M/V948R) in complex with LN3844 (PDB entry 6WXN)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 328 residues
Sequence: SGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.208
R free: 0.2355
Average B factor: 35.3366
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M BisTris, 25% PEG-3350
Matthews coefficient: 2.11
Solvent content (%): 41.72
Ligand: N-(3-{5-[2-(acetylamino)pyridin-4-yl]-2-(methylsulfanyl)-1H-imidazol-4-yl}phenyl)-2-[(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)methyl]-6-fluoro-3-hydroxybenzamide (UEJ)
Ligand formula: C33 H25 F N6 O5 S
Ligand molecular weight: 636.652
Ligand SMILES: CC(=O)Nc1cc(ccn1)c2c(nc([nH]2)SC)c3cccc(c3)NC(=O)c4c(ccc(c4CN5C(=O)c6ccccc6C5=O)O)F
Ligand InChI: InChI=1S/C33H25FN6O5S/c1-17(41)36-26-15-19(12-13-35-26)29-28(38-33(39-29)46-2)18-6-5-7-20(14-18)37-30(43)27-23(25(42)11-10-24(27)34)16-40-31(44)21-8-3-4-9-22(21)32(40)45/h3-15,42H,16H2,1-2H3,(H,37,43)(H,38,39)(H,35,36,41)
Release date: 2021-05-19
CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)-methanone (PDB entry 5IDN)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 370 residues
Sequence: DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.21989
R free: 0.25299
Average B factor: 38.236
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.2 M sodium formate, pH 6.9
Matthews coefficient: 3.1
Solvent content (%): 59.6
Ligand: [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)methanone (6A7)
Ligand formula: C18 H17 Cl N4 O
Ligand molecular weight: 340.807
Ligand SMILES: Cc1c2cc(cnc2[nH]n1)C(=O)N3CCCC3c4ccc(cc4)Cl
Ligand InChI: InChI=1S/C18H17ClN4O/c1-11-15-9-13(10-20-17(15)22-21-11)18(24)23-8-2-3-16(23)12-4-6-14(19)7-5-12/h4-7,9-10,16H,2-3,8H2,1H3,(H,20,21,22)/t16-/m0/s1
Release date: 2016-12-21
Crystal structure of human MMP-2 catalytic domain in complex with inhibitor (PDB entry 7XJO)
Macromolecule: RYH-KFB-GLU-ASP-DAB-LEU-EME-EOE-NH2
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 9 residues
Sequence: XXEDALXXX
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.19897
R free: 0.24285
Average B factor: 20.56
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20 % w/v Polyethylene glycol 3,350,  100 mM BIS-TRIS propane pH 7.5,  200mM Potassium Sodium tartrate
Matthews coefficient: 2.91
Solvent content (%): 57.73
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: 2022-06-29
Crystal structure of SETDB1 with a modified H3 peptide (PDB entry 6BHE)
Macromolecule: Histone-lysine N-methyltransferase SETDB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 239 residues
Sequence: MHHHHHHSSGRENLYFQGGELSKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMKTSSASALE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.35
R work: 0.1345
R free: 0.1725
Average B factor: 19.566
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol
Matthews coefficient: 2.26
Solvent content (%): 45.56
Ligand: UNKNOWN ATOM OR ION (UNX)
Ligand formula: X
Ligand SMILES: *
Release date: 2017-12-06
CRYSTAL STRUCTURE OF PI3K ALPHA IN COMPLEX WITH A 7-(3-(PIPERAZIN-1-YL)PHENYL)PYRROLO[2,1-F][1,2,4] TRIAZIN-4-AMINE DERIVIATINE (PDB entry 5UBR)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 944 residues
Sequence: NREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2
R free: 0.246
Average B factor: 67.31
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Matthews coefficient: 2.65
Solvent content (%): 53.6
Ligand: 1-[4-(3-{4-amino-5-[1-(oxan-4-yl)-1H-pyrazol-5-yl]pyrrolo[2,1-f][1,2,4]triazin-7-yl}phenyl)piperazin-1-yl]ethan-1-one (85S)
Ligand formula: C26 H30 N8 O2
Ligand molecular weight: 486.569
Ligand SMILES: CC(=O)N1CCN(CC1)c2cccc(c2)c3cc(c4n3ncnc4N)c5ccnn5C6CCOCC6
Ligand InChI: InChI=1S/C26H30N8O2/c1-18(35)31-9-11-32(12-10-31)21-4-2-3-19(15-21)24-16-22(25-26(27)28-17-30-34(24)25)23-5-8-29-33(23)20-6-13-36-14-7-20/h2-5,8,15-17,20H,6-7,9-14H2,1H3,(H2,27,28,30)
Release date: 2017-02-08
Structure of CHK1 10-pt. mutant complex with aminopyrimido-benzodiazepinone LRRK2 inhibitor (PDB entry 5OOT)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1757
R free: 0.2237
Average B factor: 40.023
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
Matthews coefficient: 2.36
Solvent content (%): 47.97
Ligand: 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one (4K4)
Ligand formula: C31 H38 N8 O3
Ligand molecular weight: 570.685
Ligand SMILES: CN1CCN(CC1)C2CCN(CC2)C(=O)c3ccc(c(c3)OC)Nc4ncc5c(n4)N(c6ccccc6C(=O)N5C)C
Ligand InChI: InChI=1S/C31H38N8O3/c1-35-15-17-38(18-16-35)22-11-13-39(14-12-22)29(40)21-9-10-24(27(19-21)42-4)33-31-32-20-26-28(34-31)36(2)25-8-6-5-7-23(25)30(41)37(26)3/h5-10,19-20,22H,11-18H2,1-4H3,(H,32,33,34)
Release date: 2017-10-25
uPA-BB2-94F (PDB entry 5ZAG)
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): 1.95
R work: 0.196
R free: 0.225
Average B factor: 37.55
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: 2.15
Solvent content (%): 42.79
Ligand: 3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-pyrimidin-5-yl-pyrazine-2-carboxamide (94I)
Ligand formula: C16 H21 N9 O
Ligand molecular weight: 355.398
Ligand SMILES: c1c(cncn1)c2c(nc(c(n2)C(=O)NC(=N)N)N)N3CCCCCC3
Ligand InChI: InChI=1S/C16H21N9O/c17-13-12(15(26)24-16(18)19)22-11(10-7-20-9-21-8-10)14(23-13)25-5-3-1-2-4-6-25/h7-9H,1-6H2,(H2,17,23)(H4,18,19,24,26)
Release date: 2018-12-19
Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP244 (PDB entry 6BMR)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.205
R work: 0.167
R free: 0.224
Average B factor: 40.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG3350, 200MM AMMONIUM PHOSPHATE
Matthews coefficient: 2.29
Solvent content (%): 46.22
Ligand: 4-[(2-chlorophenyl)methyl]-1-(2-hydroxy-3-methoxyphenyl)[1,2,4]triazolo[4,3-a]quinazolin-5(4H)-one (DZV)
Ligand formula: C23 H17 Cl N4 O3
Ligand molecular weight: 432.859
Ligand SMILES: COc1cccc(c1O)c2nnc3n2-c4ccccc4C(=O)N3Cc5ccccc5Cl
Ligand InChI: InChI=1S/C23H17ClN4O3/c1-31-19-12-6-9-16(20(19)29)21-25-26-23-27(13-14-7-2-4-10-17(14)24)22(30)15-8-3-5-11-18(15)28(21)23/h2-12,29H,13H2,1H3
Release date: 2018-01-17
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 8 (PDB entry 8BOH)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.158
R free: 0.1742
Average B factor: 22.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 37,5 % Precipitant Mix 4 (25% (v/v) Hexylene glycol, 25% (w/v) Poly(ethylene glycol) 1000, 25% (w/v) Poly(ethylene glycol) 3350), 
0.1M Tris-HCl pH 6.5, 
0.1 M Amino acids mix (0.2 M DL-Alanine,
0.2M DL-Glutamic acid monohydrate, 0.2M
DL-Lysine monohydrochloride, 0.2M
DL-Serine, 0.2M Glycine)
Matthews coefficient: 1.94
Solvent content (%): 36.48
Ligand: 4-methyl-~{N}-[3-(4-methylimidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide (R0T)
Ligand formula: C30 H24 F3 N9 O
Ligand molecular weight: 583.566
Ligand SMILES: Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5cc(cc(c5)n6cc(nc6)C)C(F)(F)F
Ligand InChI: InChI=1S/C30H24F3N9O/c1-17-6-7-19(29(43)37-22-10-21(30(31,32)33)11-23(12-22)42-15-18(2)35-16-42)9-25(17)38-27-24-14-36-41(3)28(24)40-26(39-27)20-5-4-8-34-13-20/h4-16H,1-3H3,(H,37,43)(H,38,39,40)
Release date: 2023-03-08
Argonaute-2 - 5'-(E)-vinylphosphonate 2'-O-methyl-uridine modified mrTTR guide RNA complex (PDB entry 5T7B)
Macromolecule: RNA (UVP)UAUAGAGCAAGAACACUGUU
Type: RNA, polyribonucleotide
Source organism: Mus musculus
Sequence length: 21 residues
Sequence: XUAUAGAGCAAGAACACUGUU
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.529
R work: 0.1935
R free: 0.2383
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 290
Crystal growth procedure: 100 mM Tris pH=9.0, 10% PEG 3350 (w/v), 8% 2-propanol (v/v), 0.12 M phenol
Matthews coefficient: 2.24
Solvent content (%): 44.97
Ligand: PHENOL (IPH)
Ligand formula: C6 H6 O
Ligand molecular weight: 94.111
Ligand SMILES: c1ccc(cc1)O
Ligand InChI: InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
Release date: 2016-12-14
The Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)-2-(5-chlorothiophen-2-yl)butanoyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid (PDB entry 8CCE)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1977
R free: 0.2337
Average B factor: 22.432
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate
Matthews coefficient: 2.29
Solvent content (%): 46.36
Ligand: 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-(5-chloranylthiophen-2-yl)butanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid (UCF)
Ligand formula: C33 H38 Cl N O8 S
Ligand molecular weight: 644.175
Ligand SMILES: CCC(c1ccc(s1)Cl)C(=O)N2CCCCC2C(=O)OC(CCc3ccc(c(c3)OC)OC)c4cccc(c4)OCC(=O)O
Ligand InChI: InChI=1S/C33H38ClNO8S/c1-4-24(29-15-16-30(34)44-29)32(38)35-17-6-5-10-25(35)33(39)43-26(22-8-7-9-23(19-22)42-20-31(36)37)13-11-21-12-14-27(40-2)28(18-21)41-3/h7-9,12,14-16,18-19,24-26H,4-6,10-11,13,17,20H2,1-3H3,(H,36,37)/t24-,25+,26-/m1/s1
Release date: 2023-04-26
Structure of DYRK1A in complex with compound 10 (PDB entry 7AJ5)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1716
R free: 0.2016
Average B factor: 39.5
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG3350, 0.1M MES buffer pH6.5, 0.2M MgCl2
Matthews coefficient: 2.49
Solvent content (%): 50.56
Ligand: 4-(1-benzofuran-5-yl)pyridine-2,6-diamine (RHW)
Ligand formula: C13 H11 N3 O
Ligand molecular weight: 225.246
Ligand SMILES: c1cc2c(cco2)cc1c3cc(nc(c3)N)N
Ligand InChI: InChI=1S/C13H11N3O/c14-12-6-10(7-13(15)16-12)8-1-2-11-9(5-8)3-4-17-11/h1-7H,(H4,14,15,16)
Release date: 2021-05-26