satarupa22/MacromolecularLigandDB huggingface dataset:
The structure of cyclin-dependent kinase 2 (CDK2) in complex with Compound 1 (PDB entry 7VDU)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 300 residues
Sequence: GAMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1764
R free: 0.2175
Average B factor: 24.955
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 12% (w/v)  PEG 3350, 0.10  M  MES pH=7.00
Matthews coefficient: 2.07
Solvent content (%): 40.74
Ligand: [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol (65L)
Ligand formula: C23 H23 F N6 O2
Ligand molecular weight: 434.466
Ligand SMILES: c1cc(c(cc1n2ccc(n2)CO)F)Nc3cc4c(ccc(n4)OC5CCNCC5)cn3
Ligand InChI: InChI=1S/C23H23FN6O2/c24-19-11-17(30-10-7-16(14-31)29-30)2-3-20(19)27-22-12-21-15(13-26-22)1-4-23(28-21)32-18-5-8-25-9-6-18/h1-4,7,10-13,18,25,31H,5-6,8-9,14H2,(H,26,27)
Release date: 2022-03-09
Crystal Structure of human phosphodiesterase 10 in complex with 2-methyl-4-(2-methylpyrrolidine-1-carbonyl)-N-(2-phenylimidazo[1,2-a]pyridin-7-yl)pyrazole-3-carboxamide (PDB entry 5SIO)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1842
R free: 0.2334
Average B factor: 44.533
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.63
Solvent content (%): 53.27
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: 2022-10-12
Crystal structure of D176N-Y306F HDAC8 in complex with a tetrapeptide substrate (PDB entry 5DC6)
Macromolecule: Histone deacetylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 389 residues
Sequence: MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVNLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGFNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.553
R work: 0.1467
R free: 0.1663
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 289
Crystal growth procedure: 100 mM Tris (pH 8.0), 13% (w/v) PEG 8000, and 4 mM TCEP
Matthews coefficient: 2.39
Solvent content (%): 48.59
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: 2016-02-03
Cathepsin-K in complex with fluoro-oxa-azabicyclo[3.3.0]octanyl containing inhibitor (PDB entry 6QLX)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 216 residues
Sequence: RAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1858
R free: 0.2373
Average B factor: 22.475
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.1
Crystallization temperature (K): 291
Crystal growth procedure: 25mM ADA pH6.1, 400mM sodium chloride and 20% PEG 5k.mme
Matthews coefficient: 2.92
Solvent content (%): 57.87
Ligand: ~{N}-[(2~{S})-1-[(3~{R},3~{a}~{R},6~{S},6~{a}~{S})-6-fluoranyl-3-oxidanyl-2,3,3~{a},5,6,6~{a}-hexahydrofuro[3,2-b]pyrrol-4-yl]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-thiophen-2-yl-benzamide (HKH)
Ligand formula: C23 H27 F N2 O4 S
Ligand molecular weight: 446.535
Ligand SMILES: CC(C)CC(C(=O)N1CC(C2C1C(CO2)O)F)NC(=O)c3ccc(cc3)c4cccs4
Ligand InChI: InChI=1S/C23H27FN2O4S/c1-13(2)10-17(23(29)26-11-16(24)21-20(26)18(27)12-30-21)25-22(28)15-7-5-14(6-8-15)19-4-3-9-31-19/h3-9,13,16-18,20-21,27H,10-12H2,1-2H3,(H,25,28)/t16-,17-,18-,20+,21+/m0/s1
Release date: 2020-02-19
Crystal Structure of human RIPK1 kinase domain in complex with a novel inhibitor (PDB entry 7FCZ)
Macromolecule: Receptor-interacting serine/threonine-protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: GASMQPDMSLNVIKMKSSDFLESAELDSGGFGKVSLAFHRTQGLMIMKTVYKGPNCIEHNEALLEEAKMMNRLRHSRVVKLLGVIIEEGKYSLVMEYMEKGNLMHVLKAEMSTPLSVKGRIILEIIEGMAYLHGKGVIHKDLKPENILVDNDFHIKIADLGLASFKMWSKLNNEEHNELREVDGTAKKNGGTLYYMAPEHLNDVNAKPTEKSDVYSFAVVLWAIFANKEPYENAIAEQQLIMAIKSGNRPDVDDITEYCPREIISLMKLCWEANPEARPTFPGIEEKFRPFYLSQLE
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.2345
R free: 0.2567
Average B factor: 38.4808
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.25 M ammonium iodide, 0.03 M glycyl-glycyl-glycine and 15-25% PEG3350.
Matthews coefficient: 2.09
Solvent content (%): 41.21
Ligand: N-[(3S)-7-(2-cyclopropylethynyl)-5-methyl-4-oxidanylidene-2,3-dihydro-1,5-benzoxazepin-3-yl]-5-(phenylmethyl)-4H-1,2,4-triazole-3-carboxamide (3IF)
Ligand formula: C25 H23 N5 O3
Ligand molecular weight: 441.482
Ligand SMILES: CN1c2cc(ccc2OCC(C1=O)NC(=O)c3[nH]c(nn3)Cc4ccccc4)C#CC5CC5
Ligand InChI: InChI=1S/C25H23N5O3/c1-30-20-13-18(10-9-16-7-8-16)11-12-21(20)33-15-19(25(30)32)26-24(31)23-27-22(28-29-23)14-17-5-3-2-4-6-17/h2-6,11-13,16,19H,7-8,14-15H2,1H3,(H,26,31)(H,27,28,29)/t19-/m0/s1
Release date: 2022-01-19
MET Tyrosine Kinase Inhibition Enhances the Antitumor Efficacy of an HGF Antibody (PDB entry 6UBW)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 343 residues
Sequence: GAMGSQVQYPLTDMSPILTSGDSDISSPLLQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVNATYVNVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1868
R free: 0.2246
Average B factor: 42.276
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 12% isopropanol, 10% PEG5000 MME, 0.06 M HEPES sodium, 0.04 M HEPES
Matthews coefficient: 2.09
Solvent content (%): 41.21
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2020-02-12
Aurora A kinase in complex with TPX2-inhibitor 9 (PDB entry 8C14)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 272 residues
Sequence: GSMGSKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1809
R free: 0.1944
Average B factor: 42.85
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 5% DMSO, 0.2M MgSO4, 0.05 M HEPES 7.4: soaking: 0.2M MgSO4, 0.05M HEPES 7.4, 30% glycerol, 10% DMSO, 5 mM compound
Matthews coefficient: 3.6
Solvent content (%): 65.8
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: 2024-01-10
Crystal structure of human KDM4A in complex with compound 17b (PDB entry 6H4X)
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): 2.34
R work: 0.166
R free: 0.207
Average B factor: 61.52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
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: 2.46
Solvent content (%): 50.04
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2019-06-12
STRUCTURE OF ALDO-KETO REDUCTASE 1C3 (AKR1C3) IN COMPLEX WITH AN INHIBITOR MEDS765 (PDB entry 9FFD)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 323 residues
Sequence: MDSKQQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1608
R free: 0.1965
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 279
Crystal growth procedure: 0.1 M MES, 24% PEG3350, PH 6.0
Matthews coefficient: 2.3
Solvent content (%): 46.42
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: 2024-08-21
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with PCM-0102197-001 (PDB entry 7G9E)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.151
R work: 0.2197
R free: 0.2918
Average B factor: 47.74
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.49
Solvent content (%): 50.51
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2023-07-12
The Structure of CK2alpha with CCh503 bound (PDB entry 6FVF)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.2
R free: 0.222
Average B factor: 34.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.01
Solvent content (%): 38.67
Ligand: [1-[2-(phenylsulfonylamino)ethyl]piperidin-4-yl]methyl 5-fluoranyl-2-methoxy-1~{H}-indole-3-carboxylate (503)
Ligand formula: C24 H28 F N3 O5 S
Ligand molecular weight: 489.56
Ligand SMILES: COc1c(c2cc(ccc2[nH]1)F)C(=O)OCC3CCN(CC3)CCNS(=O)(=O)c4ccccc4
Ligand InChI: InChI=1S/C24H28FN3O5S/c1-32-23-22(20-15-18(25)7-8-21(20)27-23)24(29)33-16-17-9-12-28(13-10-17)14-11-26-34(30,31)19-5-3-2-4-6-19/h2-8,15,17,26-27H,9-14,16H2,1H3
Release date: 2019-06-19
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 4-Pyridylthiourea (N06275b) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) (PDB entry 5FZB)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRLKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.194
R free: 0.2274
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: 2.17
Solvent content (%): 43.28
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: 2016-03-30
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 4a (PDB entry 5NKB)
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): 1.5
R work: 0.159
R free: 0.191
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD/PEG1000/PEG3350 (MD), 0.1 M Amino Acids Mix (MD), 0.1 M Hepes pH6.5
Matthews coefficient: 1.97
Solvent content (%): 37.43
Ligand: ~{N}-(2-chloranyl-6-methyl-phenyl)-2-[(3,5-dimorpholin-4-ylphenyl)amino]-1,3-thiazole-5-carboxamide (8ZT)
Ligand formula: C25 H28 Cl N5 O3 S
Ligand molecular weight: 514.04
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cc(cc(c3)N4CCOCC4)N5CCOCC5)Cl
Ligand InChI: InChI=1S/C25H28ClN5O3S/c1-17-3-2-4-21(26)23(17)29-24(32)22-16-27-25(35-22)28-18-13-19(30-5-9-33-10-6-30)15-20(14-18)31-7-11-34-12-8-31/h2-4,13-16H,5-12H2,1H3,(H,27,28)(H,29,32)
Release date: 2017-06-07
chimera of the inactive ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, with the double mutation K3528M and K3535I, fused to a proline-Rich-Domain (PRD) and profilin, bound to Latrunculin B-ADP-Mg-actin (PDB entry 8BJH)
Macromolecule: Actin, alpha skeletal muscle, intermediate form
Type: Protein, polypeptide(L)
Source organism: Oryctolagus cuniculus
Sequence length: 375 residues
Sequence: DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1783
R free: 0.2118
Average B factor: 34.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG4000 0.2M LISO4 0.1M TRIS PH8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Matthews coefficient: 2.24
Solvent content (%): 45.18
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2023-09-20
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CCL2, beta, gamma dATP analogue (PDB entry 6CRC)
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): 2.3
R work: 0.2065
R free: 0.285
Average B factor: 40.8377
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.39
Solvent content (%): 48.64
Ligand: 2'-deoxy-5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine (VA7)
Ligand formula: C11 H16 Cl2 N5 O11 P3
Ligand molecular weight: 558.099
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O)N
Ligand InChI: InChI=1S/C11H16Cl2N5O11P3/c12-11(13,30(20,21)22)31(23,24)29-32(25,26)27-2-6-5(19)1-7(28-6)18-4-17-8-9(14)15-3-16-10(8)18/h3-7,19H,1-2H2,(H,23,24)(H,25,26)(H2,14,15,16)(H2,20,21,22)/t5-,6+,7+/m0/s1
Release date: 2018-07-25
Crystal structure of SETDB1 Tudor domain with aryl triazole fragments (PDB entry 6AU2)
Macromolecule: Histone-lysine N-methyltransferase SETDB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 213 residues
Sequence: ENLYFQGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1885
R free: 0.208
Average B factor: 23.047
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG3350, 0.2M LiSO4, 0.1M Bis-Tris pH 6.5
Matthews coefficient: 2.45
Solvent content (%): 49.82
Ligand: 1-methyl-4H,6H-[1,2,4]triazolo[4,3-a][4,1]benzoxazepine (CGJ)
Ligand formula: C11 H11 N3 O
Ligand molecular weight: 201.225
Ligand SMILES: Cc1nnc2n1-c3ccccc3COC2
Ligand InChI: InChI=1S/C11H11N3O/c1-8-12-13-11-7-15-6-9-4-2-3-5-10(9)14(8)11/h2-5H,6-7H2,1H3
Release date: 2017-10-11
HBO1 is required for the maintenance of leukaemia stem cells (PDB entry 6MAK)
Macromolecule: Histone acetyltransferase KAT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 279 residues
Sequence: MGSMIKTIAFGRYELDTWYHSPYPEEYARLGRLYMCEFCLKYMKSQTILRRHMAKCVWKHPPGDEIYRKGSISVFEVDGKKNKIYCQNLCLLAKLFLDHKTLYYDVEPFLFYVMTEADNTGCHLIGYFSKEKNSFLNYNVSCILTMPQYMRQGYGKMLIDFSYLLSKVEEKVGSPERPLSDLGLISYRSYWKEVLLRYLHNFQGKEISIKEISQETAVNPVDIVSTLQALQMLKYWKGKHLVLKRQDLIDEWIAKEAKRSNSNKTMDPSCLKWTPPKAS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.21366
R free: 0.26434
Average B factor: 59.159
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Protein at 2.5 mg/mL was added in equal volume ratio with reservoir, 200 nL plus 200 nL. The reservoir consisted of 22% PEG MME 2000 plus 57 mM diammonium tartrate. Plates were stored at 20 C.
Matthews coefficient: 2.35
Solvent content (%): 47.58
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: 2019-12-25
Crystal structure of the kinase domain of TRAF2 and NCK-interacting protein kinase with NCB-0846 (PDB entry 5D7A)
Macromolecule: TRAF2 and NCK-interacting protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 308 residues
Sequence: GSGADEIDLSALRDPAGIFELVELVGNGTYGQVYKGRHVKTGQLAAIKVMDVTGDEEEEIKQEINMLKKYSHHRNIATYYGAFIKKNPPGMDDQLWLVMEFCGAGSVTDLIKNTKGNTLKEEWIAYICREILRGLSHLHQHKVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDFKSDLWSLGITAIEMAEGAPPLCDMHPMRALFLIPRNPAPRLKSKKWSKKFQSFIESCLVKNHSQRPATEQLMKHPFIRDQPNERQVRIQLKDHIDRTKKKRG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.1842
R free: 0.2391
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M Ammonium sulfate
0.1M Bis-tris (5.6)
15% PEG3350
7% Ethyleneglycol
Matthews coefficient: 3.13
Solvent content (%): 60.71
Ligand: cis-4-{[2-(1H-benzimidazol-5-ylamino)quinazolin-8-yl]oxy}cyclohexanol (58C)
Ligand formula: C21 H21 N5 O2
Ligand molecular weight: 375.424
Ligand SMILES: c1cc2cnc(nc2c(c1)OC3CCC(CC3)O)Nc4ccc5c(c4)nc[nH]5
Ligand InChI: InChI=1S/C21H21N5O2/c27-15-5-7-16(8-6-15)28-19-3-1-2-13-11-22-21(26-20(13)19)25-14-4-9-17-18(10-14)24-12-23-17/h1-4,9-12,15-16,27H,5-8H2,(H,23,24)(H,22,25,26)/t15-,16+
Release date: 2016-08-17