satarupa22/MacromolecularLigandDB huggingface dataset:
Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103007 (PDB entry 5QIX)
Macromolecule: Ubiquitin thioesterase OTUB2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 225 residues
Sequence: FNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.1471
R free: 0.1978
Average B factor: 14.222
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT
Matthews coefficient: 2.37
Solvent content (%): 48.15
Ligand: N-(3-phenylprop-2-yn-1-yl)acetamide (J5V)
Ligand formula: C11 H11 N O
Ligand molecular weight: 173.211
Ligand SMILES: CC(=O)NCC#Cc1ccccc1
Ligand InChI: InChI=1S/C11H11NO/c1-10(13)12-9-5-8-11-6-3-2-4-7-11/h2-4,6-7H,9H2,1H3,(H,12,13)
Release date: 2019-12-18
Crystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-41 (PDB entry 7COZ)
Macromolecule: Glutaminyl-peptide cyclotransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.5
Sequence length: 327 residues
Sequence: AWPEEKNYHQPAILNSSALRQIAEGTSISEMWQNDLQPLLIERYPGSPGSYAARQHIMQRIQRLQADWVLEIDTFLSQTPEGERSFSNIISTLNPTAKRHLVLACHYDSKYFSHWNNRVFVGATDSAVPCAMMLELARALDKKLLSLKTVSDSKPDLSLQLIFFDGEEAFLHWSPQDSLYGSRHLAAKMASTPHPPGARGTSQLHGMDLLVLLDLIGAPNPTFPNFFPNSARWFERLQAIEHELHELGLLKDHSLEGRYFQNYSYGGVIQDDHIPFLRRGVPVLHLIPSPFPEVWHTMDDNEENLDESTIDNLNKILQVFVLEYLHL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1955
R free: 0.2362
Average B factor: 20.7969
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 100 mM MES buffer pH 6.0-6.5, 46-67 mM NaOH, 100 mM ammonium sulfate
Matthews coefficient: 2.72
Solvent content (%): 54.85
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: 2021-01-13
Crystal structure of human ARH3-D77A bound to magnesium and ADP-ribose (PDB entry 7L9H)
Macromolecule: ADP-ribose glycohydrolase ARH3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 366 residues
Sequence: GPHMAAAAMAAAAGGGAGAARSLSRFRGCLAGALLGDCVGSFYEAHDTVDLTSVLRHVQSLEPDPGTPGSERTEALYYTADTAMARALVQSLLAKEAFDEVDMAHRFAQEYKKDPDRGYGAGVVTVFKKLLNPKCRDVFEPARAQFNGKGSYGNGGAMRVAGISLAYSSVQDVQKFARLSAQLTHASSLGYNGAILQALAVHLALQGESSSEHFLKQLLGHMEDLEGDAQSVLDARELGMEERPYSSRLKKIGELLDQASVTREEVVSELGNGIAAFESVPTAIYCFLRCMEPDPEIPSAFNSLQRTLIYSISLGGDTDTIATMAGAIAGAYYGMDQVPESWQQSCEGYEETDILAQSLHRVFQKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1801
R free: 0.2273
Average B factor: 22.78
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M sodium acetate buffer pH 4.5, 0.1 M MgCl2, and 22 % polyethylene glycol (PEG) 4000
Matthews coefficient: 2.23
Solvent content (%): 44.96
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: 2021-04-28
Structure of a hit for G Protein Coupled Receptor Kinase 2 (GRK2) Inhibitor for the Potential Treatment of Heart Failure (PDB entry 7K7Z)
Macromolecule: Beta-adrenergic receptor kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.15
Sequence length: 640 residues
Sequence: KKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLNHLEEARPLVEFYEEIKKYEKLETEEERVARSREIFDSYIMKELLACSHPFSKSATEHVQGHLGKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEARKKAKNKQLGHEEDYALGKDCIMHGYMSKMGNPFLTQWQRRYFYLFPNRLEWRGEGEAPQSLLTMEEIQSVEETQIKERKCLLLKIRGGKQFILQCDSDPELVQWKKELRDAYREAQQLVQRVPKMKNKPA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.60608692764
R work: 0.204642341506
R free: 0.261883490594
Average B factor: 72.4782885558
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 2% PEG 3350, 0.1M MES pH 6.5, 0.2M NaCl
Matthews coefficient: 3.04
Solvent content (%): 59.5
Ligand: 3-benzyl-7-(1H-pyrazol-4-yl)quinazolin-4(3H)-one (W4G)
Ligand formula: C18 H14 N4 O
Ligand molecular weight: 302.33
Ligand SMILES: c1ccc(cc1)CN2C=Nc3cc(ccc3C2=O)c4c[nH]nc4
Ligand InChI: InChI=1S/C18H14N4O/c23-18-16-7-6-14(15-9-20-21-10-15)8-17(16)19-12-22(18)11-13-4-2-1-3-5-13/h1-10,12H,11H2,(H,20,21)
Release date: 2020-10-28
CPS1 bound to allosteric inhibitor H3B-374 (PDB entry 6W2J)
Macromolecule: Carbamoyl-phosphate synthase [ammonia], mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.4.16
Sequence length: 1500 residues
Sequence: MTRILTAFKVVRTLKTGFGFTNVTAHQKWKFSRPGIRLLSVKAQTAHIVLEDGTKMKGYSFGHPSSVAGEVVFNTGLGGYPEAITDPAYKGQILTMANPIIGNGGAPDTTALDELGLSKYLESNGIKVSGLLVLDYSKDYNHWLATKSLGQWLQEEKVPAIYGVDTRMLTKIIRDKGTMLGKIEFEGQPVDFVDPNKQNLIAEVSTKDVKVYGKGNPTKVVAVDCGIKNNVIRLLVKRGAEVHLVPWNHDFTKMEYDGILIAGGPGNPALAEPLIQNVRKILESDRKEPLFGISTGNLITGLAAGAKTYKMSMANRGQNQPVLNITNKQAFITAQNHGYALDNTLPAGWKPLFVNVNDQTNEGIMHESKPFFAVQFHPEVTPGPIDTEYLFDSFFSLIKKGKATTITSVLPKPALVASRVEVSKVLILGSGGLSIGQAGEFDYSGSQAVKAMKEENVKTVLMNPNIASVQTNEVGLKQADTVYFLPITPQFVTEVIKAEQPDGLILGMGGQTALNCGVELFKRGVLKEYGVKVLGTSVESIMATEDRQLFSDKLNEINEKIAPSFAVESIEDALKAADTIGYPVMIRSAYALGGLGSGICPNRETLMDLSTKAFAMTNQILVEKSVTGWKEIEYEVVRDADDNCVTVCNMENVDAMGVHTGDSVVVAPAQTLSNAEFQMLRRTSINVVRHLGIVGECNIQFALHPTSMEYCIIEVNARLSRSSALASKATGYPLAFIAAKIALGIPLPEIKNVVSGKTSACFEPSLDYMVTKIPRWDLDRFHGTSSRIGSSMKSVGEVMAIGRTFEESFQKALRMCHPSIEGFTPRLPMNKEWPSNLDLRKELSEPSSTRIYAIAKAIDDNMSLDEIEKLTYIDKWFLYKMRDILNMEKTLKGLNSESMTEETLKRAKEIGFSDKQISKCLGLTEAQTRELRLKKNIHPWVKQIDTLAAEYPSVTNYLYVTYNGQEHDVNFDDHGMMVLGCGPYHIGSSVEFDWCAVSSIRTLRQLGKKTVVVNCNPETVSTDFDECDKLYFEELSLERILDIYHQEACGGCIISVGGQIPNNLAVPLYKNGVKIMGTSPLQIDRAEDRSIFSAVLDELKVAQAPWKAVNTLNEALEFAKSVDYPCLLRPSYVLSGSAMNVVFSEDEMKKFLEEATRVSQEHPVVLTKFVEGAREVEMDAVGKDGRVISHAISEHVEDAGVHSGDATLMLPTQTISQGAIEKVKDATRKIAKAFAISGPFNVQFLVKGNDVLVIECNLRASRSFPFVSKTLGVDFIDVATKVMIGENVDEKHLPTLDHPIIPADYVAIKAPMFSWPRLRDADPILRCEMASTGEVACFGEGIHTAFLKAMLSTGFKIPQKGILIGIQQSFRPRFLGVAEQLHNEGFKLFATEATSDWLNANNVPATPVAWPSQEGQNPSLSSIRKLIRDGSIDLVINLPNNNTKFVHDNYVIRRTAVDSGIPLLTNFQVTKLFAEAVQKSRKVDSKSLFHYRQYSAGKAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.1897
R free: 0.2503
Average B factor: 60.404
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: CPS1 protein was buffer exchanged into 50 mM glycyl-glycine pH 7.4, 50 mM KCl, 5% glycerol. CPS1 was concentrated to 10 mg/ml and H3B-4193 was added to a 5x excess molar ratio along with 1mM AMPPNP and 1mM NAG.  Ligand bound complex crystals grew by hanging drop vapor diffusion in 20% PEG 3350 and 0.2M trisodium citrate
Matthews coefficient: 2.8
Solvent content (%): 56.05
Ligand: (2-fluoranyl-4-methoxy-phenyl)-[(3~{R},5~{R})-4-(2-fluoranyl-4-methoxy-phenyl)carbonyl-3,5-dimethyl-piperazin-1-yl]methanone (374)
Ligand formula: C22 H24 F2 N2 O4
Ligand molecular weight: 418.434
Ligand SMILES: CC1CN(CC(N1C(=O)c2ccc(cc2F)OC)C)C(=O)c3ccc(cc3F)OC
Ligand InChI: InChI=1S/C22H24F2N2O4/c1-13-11-25(21(27)17-7-5-15(29-3)9-19(17)23)12-14(2)26(13)22(28)18-8-6-16(30-4)10-20(18)24/h5-10,13-14H,11-12H2,1-4H3/t13-,14-/m1/s1
Release date: 2021-01-13
Crystal structure of somatostatin receptor 2 (SSTR2) with peptide antagonist CYN 154806 (PDB entry 7XNA)
Macromolecule: Somatostatin receptor type 2,Endo-1,4-beta-xylanase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.8
Sequence length: 583 residues
Sequence: MKTIIALSYIFCLVFADYKDDDDGAPDMADEPLNGSHTWLSIPFDLNGSVVSTNTSNQTEPYYDLTSNAVLTFIYFVVCIIGLCGNTLVIYVILRYAKMKTITNIYILNLAIANELFMLGLPFLAMQVALEHWPFGKAICRVVMTVDGINQFTSIFCLTVMSIDRYLAVVHPIKSAKWRRPRTAKMITMAVWGVSLLVILPIMIYAGLRSNQWGRSSCTINWPGESGAWYTGFIIYTFILGFLVPLTIICLCYLFIIIKVKSASTDYWQNWTFGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDDTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVWSSKRKKSEKKVTRMVSIVVAVFIFCWLPFYIFNVSSVSMAISPTPALKGMFDFVVVLTYANSCANPILYAFLDDNFKKSFQNVLCLVKVSGTDDGERSDSKQDKSRLNETTETQRTEFLEVLFQGPHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2196
R free: 0.2904
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100-300 mM ammonium sulphate, 6-10% PEG2000, 1 mg/ml CYN 154806, and 0.1 M HEPES, pH 7.0
Matthews coefficient: 2.24
Solvent content (%): 45.18
Release date: 2022-08-03
Human GAR transformylase in complex with GAR and (S)-2-(8-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanamido)pentanedioic acid (AGF147) (PDB entry 4ZZ0)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.2.2
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1598
R free: 0.1852
Average B factor: 20.3105
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 18 % PEG4000, 2 % PEG400, 0.33 M NaCl
Matthews coefficient: 3.83
Solvent content (%): 67.91
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2016-04-20
Crystal Structure of the G3BP1 NTF2-like domain bound to the IDR1 of SARS-CoV-2 nucleocapsid protein D3L mutant (PDB entry 8TH1)
Macromolecule: Ras GTPase-activating protein-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 164 residues
Sequence: MSLNGPQNQRNAPRITFGGPSDSTSMVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFG
Oligomeric state: Hetero 8-mer
Stoichiometry: A4, B3, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.19809
R free: 0.23828
Average B factor: 28.429
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.2 M sodium thiocyanate, 20% PEG 3350
Matthews coefficient: 1.78
Solvent content (%): 30.89
Release date: 2023-12-27
Compound binding to Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2)discovered through fragment screening (PDB entry 5JAD)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: MAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.245
R free: 0.298
Average B factor: 33.676
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 297
Crystal growth procedure: 1.2M NaCl, 0.1M HEPES/NaOHpH=7.4, 28.8%w/v PEG 3350
Matthews coefficient: 2.42
Solvent content (%): 49.12
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: 2016-05-25
Crystal structure of PI3K complex with an inhibitor (PDB entry 5XGH)
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: 1048 residues
Sequence: GELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHHGGWTTKM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.97
R work: 0.2306
R free: 0.28012
Average B factor: 88.005
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.15M Lithium sulfate, 0.1M Tris-HCl pH 8.5, 28%(W/V) PEG2000MME
Matthews coefficient: 2.4
Solvent content (%): 48.68
Ligand: 3-[(4-fluorophenyl)methylamino]-5-(4-morpholin-4-ylthieno[3,2-d]pyrimidin-2-yl)phenol (84U)
Ligand formula: C23 H21 F N4 O2 S
Ligand molecular weight: 436.502
Ligand SMILES: c1cc(ccc1CNc2cc(cc(c2)O)c3nc4ccsc4c(n3)N5CCOCC5)F
Ligand InChI: InChI=1S/C23H21FN4O2S/c24-17-3-1-15(2-4-17)14-25-18-11-16(12-19(29)13-18)22-26-20-5-10-31-21(20)23(27-22)28-6-8-30-9-7-28/h1-5,10-13,25,29H,6-9,14H2
Release date: 2018-04-25
Selective inhibition of carbonic anhydrase IX activity, using compound SLC-149, displays limited anticancer effects in breast cancer cell lines (PDB entry 6NM0)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.1663
R free: 0.1803
Average B factor: 17.4209
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M Sodium citrate, 50 mM Tris-HCl, pH 7.8
Matthews coefficient: 2.13
Solvent content (%): 42.31
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: 2020-01-15
Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form I (PDB entry 5XIS)
Macromolecule: E3 ubiquitin-protein ligase RNF168
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 84 residues
Sequence: GPGHMLSKPGELRREYEEEISKVAAERRASEEEENKASEEYIQRLLAEEEEEEKRQAEKRRRAMEEQLKSDEELARKLSIDINN
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.2185
R free: 0.2451
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 15% PEG3350, 0.1 M Tris-HCl (pH 8.5), 100 mM MgCl2
Matthews coefficient: 3.02
Solvent content (%): 59.22
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: 2018-03-07
Crystal structure of hMTH1 N33G in complex with TH scaffold 1 in the presence of acetate (PDB entry 6GLR)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 182 residues
Sequence: MKHHHHHHPMSDYDIPTTENLYFQGAMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWGGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.601
R work: 0.1685
R free: 0.1988
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: crystallized in: 23-27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5

soaked in: 27% PEG3350, 0.2 M LiSO4, 0.1 M sodium acetate pH 4.5, 20% DMSO, 10 mM compound
Ligand: 4-phenylpyrimidin-2-amine (F3E)
Ligand formula: C10 H9 N3
Ligand molecular weight: 171.199
Ligand SMILES: c1ccc(cc1)c2ccnc(n2)N
Ligand InChI: InChI=1S/C10H9N3/c11-10-12-7-6-9(13-10)8-4-2-1-3-5-8/h1-7H,(H2,11,12,13)
Release date: 2019-02-20
APE1 Y269A phosphorothioate substrate complex with abasic DNA (PDB entry 6W4T)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQAPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTAMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.77
R work: 0.2214
R free: 0.2741
Average B factor: 53.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 27% PEG 3350, 100 mM Bis Tris Propane (pH 6.5), 200 mM Sodium Fluoride
Matthews coefficient: 2.96
Solvent content (%): 58.38
Release date: 2020-06-17
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000046b (PDB entry 7GSI)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.1962
R free: 0.2271
Average B factor: 36.229
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.29
Solvent content (%): 62.6
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Crystal structure of human DYRK1A in complex with ARN25068 (PDB entry 7OY6)
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: SSHKKERKVYNDGYDDDNYDYIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.1981
R free: 0.2704
Average B factor: 63.943
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 293
Crystal growth procedure: 15-20% PEG1000, 50 mM Mes 6.4, 100 mM KCl
Matthews coefficient: 2.56
Solvent content (%): 52.03
Ligand: ~{N}4-(3-cyclopropyl-1~{H}-pyrazol-5-yl)-~{N}2-(phenylmethyl)thieno[3,2-d]pyrimidine-2,4-diamine (39I)
Ligand formula: C19 H18 N6 S
Ligand molecular weight: 362.451
Ligand SMILES: c1ccc(cc1)CNc2nc3ccsc3c(n2)Nc4cc(n[nH]4)C5CC5
Ligand InChI: InChI=1S/C19H18N6S/c1-2-4-12(5-3-1)11-20-19-21-14-8-9-26-17(14)18(23-19)22-16-10-15(24-25-16)13-6-7-13/h1-5,8-10,13H,6-7,11H2,(H3,20,21,22,23,24,25)
Release date: 2022-03-02
Human thymine DNA glycosylase N140A mutant bound to DNA with 2'-F-5-carboxyl-dC substrate analog (PDB entry 6U15)
Macromolecule: G/T mismatch-specific thymine DNA glycosylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.29
Sequence length: 227 residues
Sequence: SKKSGKSAKSKEKQEKITDTFKVKRKVDRFNGVSEAELLTKTLPDILTFNLDIVIIGIAPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.199
R free: 0.213
Average B factor: 65.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: PEG 3350, Ammonium Acetate, Sodium Acetate
Matthews coefficient: 2.38
Solvent content (%): 48.22
Release date: 2019-11-20