satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of aminopeptidase ERAP2 with ligand (PDB entry 5AB0)
Macromolecule: ENDOPLASMATIC RETICULUM AMINOPEPTIDASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.1
Sequence length: 967 residues
Sequence: MFHSSAMVNSHRKPMFNIHRGFYCLTAILPQICICSQFSVPSSYHFTEDPGAFPVATNGERFPWQELRLPSVVIPLHYDLFVHPNLTSLDFVASEKIEVLVSNATQFIILHSKDLEITNATLQSEEDSRYMKPGKELKVLSYPAHEQIALLVPEKLTPHLKYYVAMDFQAKLGDGFEGFYKSTYRTLGGETRILAVTDFEPTQARMAFPCFDEPLFKANFSIKIRRESRHIALSNMPKVKTIELEGGLLEDHFETTVKMSTYLVAYIVCDFHSLSGFTSSGVKVSIYASPDKRNQTHYALQASLKLLDFYEKYFDIYYPLSKLDLIAIPDFAPGAMENWGLITYRETSLLFDPKTSSASDKLWVTRVIAHELAHQWFGNLVTMEWWNDIWLNEGFAKYMELIAVNATYPELQFDDYFLNVCFEVITKDSLNSSRPISKPAETPTQIQEMFDEVSYNKGACILNMLKDFLGEEKFQKGIIQYLKKFSYRNAKNDDLWSSLSNSCLESDFTSGGVCHSDPKMTSNMLAFLGENAEVKEMMTTWTLQKGIPLLVVKQDGCSLRLQQERFLQGVFQEDPEWRALQERYLWHIPLTYSTSSSNVIHRHILKSKTDTLDLPEKTSWVKFNVDSNGYYIVHYEGHGWDQLITQLNQNHTLLRPKDRVGLIHDVFQLVGAGRLTLDKALDMTYYLQHETSSPALLEGLSYLESFYHMMDRRNISDISENLKRYLLQYFKPVIDRQSWSDKGSVWDRMLRSALLKLACDLNHAPCIQKAAELFSQWMESSGKLNIPTDVLKIVYSVGAQTTAGWNYLLEQYELSMSSAEQNKILYALSTSKHQEKLLKLIELGMEGKVIKTQNLAALLHAIARRPKGQQLAWDFVRENWTHLLKKFDLGSYDIRMIISGTTAHFSSKDKLQEVKLFFESLEAQGSHLDIFQTVLETITKNIKWLEKNLPTLRTWLMVNTRHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1981
R free: 0.258
Average B factor: 56.3
Crystallization pH: 6.3
Crystal growth procedure: 6 %(W/V) PEG MW 8000, 25 %(V/V) ETHYLENE GLYCOL, 59 MM MES AND 41 MM IMIDAZOLE AT PH 6.3
Matthews coefficient: 2.19
Solvent content (%): 38.45
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: 2015-09-30
BACE crystal structure with tricyclic aminothiazine inhibitor (PDB entry 4ZSR)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 442 residues
Sequence: MAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.18752
R free: 0.20348
Average B factor: 15.61
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: PEG8000, sodium cacodylate, ammonium sulfate
Matthews coefficient: 2.6
Solvent content (%): 52.77
Ligand: N-[(4aS,6S,8aR)-2-amino-5,6,7,8-tetrahydro-4a,8a-(methanooxymethano)-3,1-benzothiazin-6(4H)-yl]-3-chlorobenzamide (4RY)
Ligand formula: C17 H20 Cl N3 O2 S
Ligand molecular weight: 365.878
Ligand SMILES: c1cc(cc(c1)Cl)C(=O)NC2CCC34COCC3(C2)CSC(=N4)N
Ligand InChI: InChI=1S/C17H20ClN3O2S/c18-12-3-1-2-11(6-12)14(22)20-13-4-5-17-9-23-8-16(17,7-13)10-24-15(19)21-17/h1-3,6,13H,4-5,7-10H2,(H2,19,21)(H,20,22)/t13-,16-,17-/m0/s1
Release date: 2015-06-10
Crystal structure of the second bromodomain (BD2) of human TAF1 bound to ATR kinase inhibitor AZ20 (PDB entry 7JJG)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 137 residues
Sequence: SMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1688
R free: 0.1948
Average B factor: 26.1453
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.01 M Co(II) chloride, 0.1 M Sodium acetate trihydrate (pH 4.6), 1 M 1,6-Hexanediol
Matthews coefficient: 2.51
Solvent content (%): 50.95
Ligand: 4-{4-[(3R)-3-methylmorpholin-4-yl]-6-[1-(methylsulfonyl)cyclopropyl]pyrimidin-2-yl}-1H-indole (VCD)
Ligand formula: C21 H24 N4 O3 S
Ligand molecular weight: 412.505
Ligand SMILES: CC1COCCN1c2cc(nc(n2)c3cccc4c3cc[nH]4)C5(CC5)S(=O)(=O)C
Ligand InChI: InChI=1S/C21H24N4O3S/c1-14-13-28-11-10-25(14)19-12-18(21(7-8-21)29(2,26)27)23-20(24-19)16-4-3-5-17-15(16)6-9-22-17/h3-6,9,12,14,22H,7-8,10-11,13H2,1-2H3/t14-/m1/s1
Release date: 2021-07-28
Crystal structure of the human PDI first domain with 9 mutations (PDB entry 8GDY)
Macromolecule: Protein disulfide-isomerase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.3.4.1
Sequence length: 141 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMDAPEEEDHVLVLRRSNFAEALAAHRYLLVEFYAPWCGHCRALAPEYARAAGRLRAEGSEIRLAKVDATEESDLAQQYGVRGYPTIKFFRNGDTASPREYTAGREADDIVNWLRRRTGPAA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1924
R free: 0.2391
Crystallization method: MICROBATCH
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M potassium thiocyanate, 0.1 M MES, and 24% (w/v) PEG 20k
Matthews coefficient: 1.95
Solvent content (%): 36.98
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: 2024-01-24
Crystal Structure of human phosphodiesterase 10 in complex with 2,3-dimethyl-6-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-8-methylsulfonylimidazo[1,2-b]pyridazine (PDB entry 5SH3)
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): 1.98
R work: 0.1705
R free: 0.2218
Average B factor: 36.297
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 (%): 53.2
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 the human CARBOXYPEPTIDASE A1 in complex with the PHOSPHINIC INHIBITOR Acetyl-Leu-Phe-Y(PO2CH2)-Phe-OH (PDB entry 4UEZ)
Macromolecule: HUMAN CARBOXYPEPTIDASE A1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.1
Sequence length: 309 residues
Sequence: ARSTDTFNYATYHTLEEIYDFLDLLVAENPHLVSKIQIGNTYEGRPIYVLKFSTGGSKRPAIWIDTGIHSREWVTQASGVWFAKKITQDYGQDAAFTAILDTLDIFLEIVTNPDGFAFTHSTNRMWRKTRSHTAGSLCIGVDPNRNWDAGFGLSGASSNPCSETYHGKFANSEVEVKSIVDFVKDHGNIKAFISIHSYSQLLMYPYGYKTEPVPDQDELDQLSKAAVTALASLYGTKFNYGSIIKAIYQASGSTIDWTYSQGIKYSFTFELRDTGRYGFLLPASQIIPTAKETWLALLTIMEHTLNHPY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.15036
R free: 0.20519
Average B factor: 9.005
Crystal growth procedure: 0.2 M CALCIUM CHLORIDE, 0.1 M HEPES PH 7.0 AND 17% W/V PEG6000
Matthews coefficient: 2.2
Solvent content (%): 44.19
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: 2016-01-20
Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60 (PDB entry 4RPU)
Macromolecule: Presequence protease, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24
Sequence length: 1014 residues
Sequence: MHHHHHHAAACERALQYKLGDKIHGFTVNQVTSVPELFLTAVKLTHDDTGARYLHLAREDTNNLFSVQFRTTPMDSTGVPHILQHTVLCGSQKYPCRDPFFKMLNRSLSTFMNAFTASDYTLYPFSTQNPKDFQNLLSVYLDATFFPCLRELDFWQEGWRLEHENPSDPQTPLVFKGVVFNEMKGAFTDNERIFSQHLQNRLLPDHTYSVVSGGDPLCIPELTWEQLKQFHATHYHPSNARFFTYGNFPLEQHLKQIHEEALSKFQKIEPSTVVPAQTPWDKPREFQITCGPDSFATDPSKQTTVSVSFLLPDITDTFEAFTLSLLSSLLTSGPNSPFYKALIESGLGTDFSPDVGYNGYTREAYFSVGLQGIVEKDIETVRSLIDRTIDEVVEKGFEDDRIEALLHKIEIQMKHQSTSFGLMLTSYIASCWNHDGDPVELLKLGNQLAKFRQCLQENPKFLQEKVKQYFKNNQHKLTLSMRPDDKYHEKQAQVEATKLKQKVEALSPGDRQQIYEKGLELRSQQSKPQDASCLPALKVSDIEPTIPVTELDVVLTAGDIPVQYCAQPTNGMVYFRAFSSLNTLPEELRPYVPLFCSVLTKLGCGLLDYREQAQQIELKTGGMSASPHVLPDDSHMDTYEQGVLFSSLCLDRNLPDMMQLWSEIFNNPCFEEEEHFKVLVKMTAQELANGIPDSGHLYASIRAGRTLTPAGDLQETFSGMDQVRLMKRIAEMTDIKPILRKLPRIKKHLLNGDNMRCSVNATPQQMPQTEKAVEDFLRSIGRSKKERRPVRPHTVEKPVPSSSGGDAHVPHGSQVIRKLVMEPTFKPWQMKTHFLMPFPVNYVGECIRTVPYTDPDHASLKILARLMTAKFLHTEIREKGGAYGGGAKLSHNGIFTLYSYRDPNTIETLQSFGKAVDWAKSGKFTQQDIDEAKLSVFSTVDAPVAPSDKGMDHFLYGLSDEMKQAHREQLFAVSHDKLLAVSDRYLGTGKSTHGLAILGPENPKIAKDPSWIIR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.265
R work: 0.1755
R free: 0.2078
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 291
Crystal growth procedure: 15.0% PEG 8000, 15 mM TCEP, 80 mM sodium cacodylate pH 6.7, 160 mM calcium acetate, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.84
Solvent content (%): 56.75
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: 2015-12-09
Structure of Pediculus humanus Parkin bound to phospho-ubiquitin (PDB entry 5CAW)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Pediculus humanus corporis
EC number: 6.3.2
Sequence length: 321 residues
Sequence: GKNKAHFFIYCANPCKKINTGKLRVCCSECKHGAFTVDTDPQSWADVLDKNKITGVCNNVGCEGLYAKFYFKCASHPSQGENDTAVPLNLIKRNHKKIPCLACTDICDPVLVFSCDNRHVTCLECFKNYCGSRLKDRQFLSHPDFGYTLPCPAGCSNSFIEEVHHFRLLTDAQYEQYHRFATEEFILQAGGVLCPQPGCGQGILIDQNCNRVQCSCGYVFCGKCLEGFHLGECLNPTDVPFLSQNCDYPLDPEKLEKARWDEASSTVIKVLTKPCPKCRTSTERAGGCMHMICTRANCGFHWCWVCQGPWERDCMASHWFG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.2276
R free: 0.2595
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 2% (v/v) PEG400, 2 M NH4SO4, 0.1 M HEPES pH 7.5
Matthews coefficient: 2.48
Solvent content (%): 50.39
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: 2015-07-22
PDGFRA wild-type kinase domain (PDB entry 8PQJ)
Macromolecule: Platelet-derived growth factor receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 352 residues
Sequence: KQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGKVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTKSGPIYIITEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLSFTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFLPVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAKPDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.1838
R free: 0.2151
Average B factor: 40.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 285.15
Crystal growth procedure: 10 mg/mL, 15% PEG3350, 100 mM Bis-Tris-Propane, pH 7.5
Matthews coefficient: 1.85
Solvent content (%): 33.47
Release date: 2023-12-27
Caspase-3 Mutant- D9A,D28A,T152D (PDB entry 6BGK)
Macromolecule: Caspase-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.56
Sequence length: 175 residues
Sequence: MENTENSVASKSIKNLEPKIIHGSESMASGISLDNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLDGKPKLFIIQACRGTELDCGIETD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.1593
R free: 0.2109
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.
Matthews coefficient: 2.18
Solvent content (%): 43.68
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: 2018-02-21
Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2149 (PDB entry 6T6D)
Macromolecule: Activin receptor type I
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): 2.56
R work: 0.2217
R free: 0.2717
Average B factor: 73.66
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.9
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 4.9, 1M ammonium sulfate, 0.2M sodium/potassium tartrate
Matthews coefficient: 2.92
Solvent content (%): 57.9
Ligand: 2-methoxy-4-[4-methyl-5-(4-piperazin-1-ylphenyl)pyridin-3-yl]benzamide (MM8)
Ligand formula: C24 H26 N4 O2
Ligand molecular weight: 402.489
Ligand SMILES: Cc1c(cncc1c2ccc(c(c2)OC)C(=O)N)c3ccc(cc3)N4CCNCC4
Ligand InChI: InChI=1S/C24H26N4O2/c1-16-21(17-3-6-19(7-4-17)28-11-9-26-10-12-28)14-27-15-22(16)18-5-8-20(24(25)29)23(13-18)30-2/h3-8,13-15,26H,9-12H2,1-2H3,(H2,25,29)
Release date: 2019-10-30
Crystal Structure of human cyclic GMP-AMP synthase in complex with 6-(2-chloro-5-fluoro-4-methylphenyl)-1H-benzimidazole-4-carboxylic acid (PDB entry 7FU2)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.249
R free: 0.287
Average B factor: 93.89
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Matthews coefficient: 2.41
Solvent content (%): 48.97
Ligand: (5M)-5-(2-chloro-5-fluoro-4-methylphenyl)-1H-benzimidazole-7-carboxylic acid (YM9)
Ligand formula: C15 H10 Cl F N2 O2
Ligand molecular weight: 304.704
Ligand SMILES: Cc1cc(c(cc1F)c2cc(c3c(c2)nc[nH]3)C(=O)O)Cl
Ligand InChI: InChI=1S/C15H10ClFN2O2/c1-7-2-11(16)9(5-12(7)17)8-3-10(15(20)21)14-13(4-8)18-6-19-14/h2-6H,1H3,(H,18,19)(H,20,21)
Release date: 2024-02-21
CDK8-CYCC IN COMPLEX WITH 8-[3-Chloro-5-(1-methyl-2,2-dioxo-2, 3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl)-pyridin- 4-yl]-1-oxa-3,8-diaza-spiro[4.5]decan-2-one (PDB entry 5HBE)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 364 residues
Sequence: DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.2287
R free: 0.2555
Average B factor: 37.069
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 293
Crystal growth procedure: RESERVOIR SOLUTION : pH 6.90
Matthews coefficient: 3.09
Solvent content (%): 60.27
Ligand: 8-[3-chloranyl-5-[1-methyl-2,2-bis(oxidanylidene)-3~{H}-2,1-benzothiazol-5-yl]pyridin-4-yl]-1-oxa-3,8-diazaspiro[4.5]decan-2-one (5Y6)
Ligand formula: C20 H21 Cl N4 O4 S
Ligand molecular weight: 448.923
Ligand SMILES: CN1c2ccc(cc2CS1(=O)=O)c3cncc(c3N4CCC5(CC4)CNC(=O)O5)Cl
Ligand InChI: InChI=1S/C20H21ClN4O4S/c1-24-17-3-2-13(8-14(17)11-30(24,27)28)15-9-22-10-16(21)18(15)25-6-4-20(5-7-25)12-23-19(26)29-20/h2-3,8-10H,4-7,11-12H2,1H3,(H,23,26)
Release date: 2016-02-03
Potent competitive inhibition of human ribonucleotide reductase by a novel non-nucleoside small molecule (PDB entry 5TUS)
Macromolecule: Ribonucleoside-diphosphate reductase large subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.17.4.1
Sequence length: 792 residues
Sequence: MHVIKRDGRQERVMFDKITSRIQKLCYGLNMDFVDPAQITMKVIQGLYSGVTTVELDTLAAETAATLTTKHPDYAILAARIAVSNLHKETKKVFSDVMEDLYNYINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGFKTLERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWFTHASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGVAVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGNKRPGAFAIYLEPWHLDIFEFLDLKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLDEVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTSEHTYDFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADAFILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAKEQGPYETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLLIAPMPTASTAQILGNNESIEPYTSNIYTRRVLSGEFQIVNPHLLKDLTERGLWHEEMKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQSLNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTRPAANPIQFTLNKEKLKDKEKVSKEEEEKERNTAAMVCSLENRDECLMCGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.66
R work: 0.19911
R free: 0.24967
Average B factor: 56.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.9
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris-HCl pH 7.9, 0.2 M LiSO4, 19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Matthews coefficient: 2.43
Solvent content (%): 49.31
Ligand: THYMIDINE-5'-TRIPHOSPHATE (TTP)
Ligand formula: C10 H17 N2 O14 P3
Ligand molecular weight: 482.168
Ligand SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
Release date: 2017-08-02
Crystal structure of the His Domain Protein Tyrosine Phosphatase (HD-PTP/PTPN23) Bro1 domain (Apo structure) (PDB entry 5MJZ)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 23
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 361 residues
Sequence: MEAVPRMPMIWLDLKEAGDFHFQPAVKKFVLKNYGENPEAYNEELKKLELLRQNAVRVPRDFEGCSVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTEIFSGKSVAHEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLREHFPQAYSVDMSRQILTLNVNLMLGQAQECLLEKSMLDNRKSFLVARISAQVVDYYKEACRALENPDTASLLGRIQKDWKKLVQMKIYYFAAVAHLHMGKQAEEQQKFGERVAYFQSALDKLNEAIKLAKGQPDTVQDALRFTMDVIGGKYNSAKKDNDFIYHEAVPALDTLQPVKGAPLVKPLPVNPTDPAVTGPDIFAKLV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.867
R work: 0.176
R free: 0.2161
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: Apo- HD-PTPBro1 crystals were obtained in 0.2M L-Na-Glutamate, 0.2M Alanine, 0.2M Glycine, 0.2M Lysine HCl, 0.2M Serine, 0.1 M Imidazole; MES monohydrate at pH 6.5 and 30% Ethylene glycol, PEG8K.
Matthews coefficient: 2.26
Solvent content (%): 45.57
Release date: 2017-08-16
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000279a (PDB entry 7GSK)
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): 1.84
R work: 0.1909
R free: 0.2356
Average B factor: 39.866
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: 3.33
Solvent content (%): 63.02
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 cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in AMP-PNP bound state (PDB entry 6BG2)
Macromolecule: cGMP-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 347 residues
Sequence: GSGLDDVSNKAYEDAEAKAKYEAEAAFFANLKLSDFNIIDTLGVGGFGRVELVQLKSEESKTFAMKILKKRHIVDTRQQEHIRSEKQIMQGAHSDFIVRLYRTFKDSKYLYMLMEACLGGELWTILRDRGSFEDSTTRFYTACVVEAFAYLHSKGIIYRDLKPENLILDHRGYAKLVDFGFAKKIGFGKKTWTFCGTPEYVAPEIILNKGHDISADYWSLGILMYELLTGSPPFSGPDPMKTYNIILRGIDMIEFPKKIAKNAANLIKKLCRDNPSERLGNLKNGVKDIQKHKWFEGFNWEGLRKGTLTPPIIPSVASPTDTSNFDSFPEDNDEPPPDDNSGWDIDF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.188
R free: 0.2155
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 23.2% PEG1500, 0.08 M PCTP, pH8.0, 0.5% w/v polyvinylpyrrolidone K15
Matthews coefficient: 2.19
Solvent content (%): 43.92
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2018-10-31