satarupa22/MacromolecularLigandDB huggingface dataset:
The X-ray structure of human M190I phosphoglycerate kinase 1 mutant (PDB entry 5MXM)
Macromolecule: Phosphoglycerate kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.2.3
Sequence length: 416 residues
Sequence: SLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLIKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.17623
R free: 0.22554
Average B factor: 22.582
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: PEG MME 30% w/v, Bis Tris 0.1 M pH=7
Matthews coefficient: 2.14
Solvent content (%): 42.5
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: 2018-02-14
Pak1 in complex with bis-anilino pyrimidine inhibitor (PDB entry 5KBQ)
Macromolecule: Serine/threonine-protein kinase PAK 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 289 residues
Sequence: LEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLDMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.175
R free: 0.23
Average B factor: 86.82
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M ammonium sulphate, 16% PEG 3350, 0.1M Hepes (pH 7.6)
Matthews coefficient: 2.5
Solvent content (%): 50.74
Ligand: [4-methyl-3-[methyl-[2-[(3-methylsulfonyl-5-morpholin-4-yl-phenyl)amino]pyrimidin-4-yl]amino]phenyl]methanol (IPV)
Ligand formula: C24 H29 N5 O4 S
Ligand molecular weight: 483.583
Ligand SMILES: Cc1ccc(cc1N(C)c2ccnc(n2)Nc3cc(cc(c3)S(=O)(=O)C)N4CCOCC4)CO
Ligand InChI: InChI=1S/C24H29N5O4S/c1-17-4-5-18(16-30)12-22(17)28(2)23-6-7-25-24(27-23)26-19-13-20(29-8-10-33-11-9-29)15-21(14-19)34(3,31)32/h4-7,12-15,30H,8-11,16H2,1-3H3,(H,25,26,27)
Release date: 2016-09-28
Ube2D1 in complex with ubiquitin variant Ubv.D1.1 (PDB entry 6D4P)
Macromolecule: Ubiquitin-conjugating enzyme E2 D1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.23
Sequence length: 149 residues
Sequence: GAMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLVPDIAQIYKSDKEKYNRHAREWTQKYAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.2142
R free: 0.231
Average B factor: 56.99
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG2000-MME, 0.2M trimethylamine N-oxide, 0.1M Tris-HCl
Matthews coefficient: 2.55
Solvent content (%): 51.82
Release date: 2019-07-17
Crystal Structure of panitumumab in complex with epidermal growth factor receptor domain 3. (PDB entry 5SX4)
Macromolecule: Panitumumab Fab Light Chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 214 residues
Sequence: DIQMTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYDASNLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQHFDHLPLAFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2233
R free: 0.2661
Average B factor: 54.6188
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.0 M AmSO4, 100 mM MES 6.5  and 5% peg 400
Matthews coefficient: 3.1
Solvent content (%): 60.27
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: 2016-10-05
HRAS R97I Crystal Form 1 (PDB entry 8ELX)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 189 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYIEQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.975
R work: 0.2273
R free: 0.2864
Average B factor: 22.1579
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: PEG 3350,
Calcium Acetate,
Magnesium Chloride,
Sodium Chloride,
DTT
Matthews coefficient: 2.43
Solvent content (%): 49.37
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2023-09-06
Crystal structure of the tandem bromodomain (BD1, BD2) of human TAF1 bound to ZS1-295 (PDB entry 7LB0)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 265 residues
Sequence: SMSIHRRRTDPMVTLSSILESIINDMRDLPNTYPFHTPVNAKVVKDYYKIITRPMDLQTLRENVRKRLYPSREEFREHLELIVKNSATYNGPKHSLTQISQSMLDLCDEKLKEKEDKLARLEKAINPLLDDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.1973
R free: 0.2199
Average B factor: 30.5345
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M MgCl2, 0.1 M Bis-Tris pH 6.5, 25% PEG 3350
Matthews coefficient: 2.46
Solvent content (%): 49.98
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: 2021-07-14
Crystal structure of CDK2 liganded with compound EF2252 (PDB entry 7S4T)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.1744
R free: 0.2185
Average B factor: 19.3452
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 4.5mg/mL CDK2,1mM EF2252 soaking 48hours at 0.1M Hepes Na, pH7.5, 10%(v/v)PEG3350
Matthews coefficient: 1.95
Solvent content (%): 36.78
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: 2022-09-21
The Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)-2-(5-chlorothiophen-2-yl)-2-(3,4,5-trimethoxyphenyl)acetyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid (PDB entry 8CCD)
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): 2.1
R work: 0.2253
R free: 0.2722
Average B factor: 45.756
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate
Matthews coefficient: 2.24
Solvent content (%): 45.01
Ligand: 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-(5-chloranylthiophen-2-yl)-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid (UCO)
Ligand formula: C40 H44 Cl N O11 S
Ligand molecular weight: 782.295
Ligand SMILES: COc1ccc(cc1OC)CCC(c2cccc(c2)OCC(=O)O)OC(=O)C3CCCCN3C(=O)C(c4ccc(s4)Cl)c5cc(c(c(c5)OC)OC)OC
Ligand InChI: InChI=1S/C40H44ClNO11S/c1-47-30-15-13-24(19-31(30)48-2)12-14-29(25-9-8-10-27(20-25)52-23-36(43)44)53-40(46)28-11-6-7-18-42(28)39(45)37(34-16-17-35(41)54-34)26-21-32(49-3)38(51-5)33(22-26)50-4/h8-10,13,15-17,19-22,28-29,37H,6-7,11-12,14,18,23H2,1-5H3,(H,43,44)/t28-,29+,37+/m0/s1
Release date: 2023-04-26
Crystal Structure of human phosphodiesterase 10 in complex with 3-[4-[2-[2-(2-ethoxy-4-fluorophenyl)-5-methyl-1,3-oxazol-4-yl]ethoxy]naphthalen-1-yl]-2-methoxypropanoic acid (PDB entry 5SKU)
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: 0.1812
R free: 0.225
Average B factor: 38.347
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: 2.62
Solvent content (%): 53.06
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: 2022-10-12
CRYSTAL STRUCTURE OF BTK IN COMPLEX WITH COVALENT FRAGMENT LIGAND (PDB entry 6DI1)
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): 1.1
R work: 0.1732
R free: 0.1861
Average B factor: 11.56
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: RESERVOIR SOLUTION : 25% PEG 3350, 0.2M AMMONIUM ACETATE, 0.1M HEPES pH 6.9, 3% GLYCEROL                      
PROTEIN SOLUTION   : 10 mg/mL IN 20 mM TRIS, 50 mM NACL, 3 mM DTT, pH 8.0
Matthews coefficient: 2.27
Solvent content (%): 45.81
Ligand: 4-amino-2-[(3S)-3-(propanoylamino)pyrrolidin-1-yl]pyrimidine-5-carboxamide (GJD)
Ligand formula: C12 H18 N6 O2
Ligand molecular weight: 278.31
Ligand SMILES: CCC(=O)NC1CCN(C1)c2ncc(c(n2)N)C(=O)N
Ligand InChI: InChI=1S/C12H18N6O2/c1-2-9(19)16-7-3-4-18(6-7)12-15-5-8(11(14)20)10(13)17-12/h5,7H,2-4,6H2,1H3,(H2,14,20)(H,16,19)(H2,13,15,17)/t7-/m0/s1
Release date: 2018-10-17
Crystal structure of chimeric carbonic anhydrase IX with inhibitor (PDB entry 4Q06)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVEFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKALQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.137
R free: 0.168
Average B factor: 17.922
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 2.03
Solvent content (%): 38.9
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: 2015-01-28
BACE1 compound 28 (PDB entry 6EJ2)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 501 residues
Sequence: MAQALPWLLLWMGAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTDLMEDCGYNIPQTDESTLMTIAYVMAAICALFMLPLCLMVCQWRCLRCLRQQHDDFADDISLLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.2063
R free: 0.2318
Average B factor: 36.19
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG 5k MME, 0.2M AmI, 0.2M sodium citrate pH 6.5
Matthews coefficient: 2.28
Solvent content (%): 46
Ligand: compound 28 (B7E)
Ligand formula: C22 H26 N4 O2
Ligand molecular weight: 378.467
Ligand SMILES: CC1CC2(CCC1OC)Cc3ccc(cc3C24COC(=N4)N)c5cncnc5
Ligand InChI: InChI=1S/C22H26N4O2/c1-14-8-21(6-5-19(14)27-2)9-16-4-3-15(17-10-24-13-25-11-17)7-18(16)22(21)12-28-20(23)26-22/h3-4,7,10-11,13-14,19H,5-6,8-9,12H2,1-2H3,(H2,23,26)/t14-,19-,21-,22-/m0/s1
Release date: 2018-04-18
The Ribosomal RNA Processing 1B Protein Phosphatase-1 Holoenzyme (PDB entry 7T0Y)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 299 residues
Sequence: GHMGSLNLDSIIGRLLEVRGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2081
R free: 0.2462
Average B factor: 27.62
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 289
Crystal growth procedure: 20% ethylene glycol; 10% PEG8000, 0.1 M imidazole; MES acid, 0.09 M Sodium fluoride; 0.09 M Sodium bromide; 0.09 M Sodium iodide
Matthews coefficient: 2.15
Solvent content (%): 42.87
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: 2022-12-07
KRAS-G13D in complex with BI-2865 (PDB entry 8B00)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGAGDVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.04
R work: 0.1439
R free: 0.161
Average B factor: 21.03
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2mM Magnesium Chloride, 20% PEG 2000, 100mM sodium acetate pH 4.4
Matthews coefficient: 2.54
Solvent content (%): 51.56
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2023-06-07
Crystal structure of JAK2 JH2 in complex with Bemcentinib (PDB entry 8BA3)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1737
R free: 0.1965
Average B factor: 26.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris pH 8, 16% PEG4000, 0.2M Na-acetate
Matthews coefficient: 2.07
Solvent content (%): 40.49
Ligand: 1-(3,4-diazatricyclo[9.4.0.0^{2,7}]pentadeca-1(11),2(7),3,5,12,14-hexaen-5-yl)-~{N}3-[(7~{S})-7-pyrrolidin-1-yl-6,7,8,9-tetrahydro-5~{H}-benzo[7]annulen-3-yl]-1,2,4-triazole-3,5-diamine (Q8U)
Ligand formula: C30 H34 N8
Ligand molecular weight: 506.645
Ligand SMILES: c1ccc-2c(c1)CCCc3c2nnc(c3)n4c(nc(n4)Nc5ccc6c(c5)CCC(CC6)N7CCCC7)N
Ligand InChI: InChI=1S/C30H34N8/c31-29-33-30(32-24-13-10-20-11-14-25(15-12-22(20)18-24)37-16-3-4-17-37)36-38(29)27-19-23-8-5-7-21-6-1-2-9-26(21)28(23)35-34-27/h1-2,6,9-10,13,18-19,25H,3-5,7-8,11-12,14-17H2,(H3,31,32,33,36)/t25-/m0/s1
Release date: 2023-02-01
Crystal Structure of human phosphodiesterase 10 in complex with 2-methyl-4-(morpholine-4-carbonyl)-N-(2-pyrrolidin-1-yl-[1,2,4]triazolo[1,5-a]pyridin-7-yl)pyrazole-3-carboxamide (PDB entry 5SJZ)
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): 2.19
R work: 0.1703
R free: 0.226
Average B factor: 46.576
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 (%): 53.25
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: 2022-10-12
Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT1982 from cocktail soak (PDB entry 6DIM)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.1863
R free: 0.2267
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M MOPS/HEPES-Na pH 7.5
10% w/v PEG 8000
20% v/v ethylene glycol
0.03M sodium fluoride
0.03M sodium bromide
0.03M sodium iodide
Matthews coefficient: 2.47
Solvent content (%): 50.3
Ligand: 4-hydroxyquinoline-3-carboxylic acid (GJP)
Ligand formula: C10 H7 N O3
Ligand molecular weight: 189.167
Ligand SMILES: c1ccc2c(c1)c(c(cn2)C(=O)O)O
Ligand InChI: InChI=1S/C10H7NO3/c12-9-6-3-1-2-4-8(6)11-5-7(9)10(13)14/h1-5H,(H,11,12)(H,13,14)
Release date: 2019-05-29
DNA polymerase beta nick complex with imidodiphosphate (PDB entry 5UGO)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACGGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.897
R work: 0.1794
R free: 0.2356
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 7.5
Matthews coefficient: 2.25
Solvent content (%): 45.32
Ligand: IMIDODIPHOSPHORIC ACID (2PN)
Ligand formula: H5 N O6 P2
Ligand molecular weight: 176.99
Ligand SMILES: N(P(=O)(O)O)P(=O)(O)O
Ligand InChI: InChI=1S/H5NO6P2/c2-8(3,4)1-9(5,6)7/h(H5,1,2,3,4,5,6,7)
Release date: 2017-07-26