satarupa22/MacromolecularLigandDB huggingface dataset:
The co-crystal structure of DYRK2 with a small molecule inhibitor 19 (PDB entry 7DHH)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 324 residues
Sequence: HDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.486
R work: 0.189
R free: 0.2453
Average B factor: 66.4537
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.36 M-0.5 M sodium citrate tribasic dehydrate, 0.01 M sodium borate, pH 7.5-9.5
Matthews coefficient: 3.67
Solvent content (%): 66.53
Ligand: [9-(azetidin-3-ylmethylsulfanyl)-2,7-dimethoxy-acridin-4-yl]methanol (H7L)
Ligand formula: C20 H22 N2 O3 S
Ligand molecular weight: 370.465
Ligand SMILES: COc1ccc2c(c1)c(c3cc(cc(c3n2)CO)OC)SCC4CNC4
Ligand InChI: InChI=1S/C20H22N2O3S/c1-24-14-3-4-18-16(6-14)20(26-11-12-8-21-9-12)17-7-15(25-2)5-13(10-23)19(17)22-18/h3-7,12,21,23H,8-11H2,1-2H3
Release date: 2021-11-17
Factor Xa complex with GTC000406 (PDB entry 4Y79)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.6
Sequence length: 254 residues
Sequence: IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKAKSHAPEVITSSPLK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1752
R free: 0.2161
Average B factor: 33.704
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.75
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG 6000,  100 mM MES PH5.75, 10 mM calcium chloride
Matthews coefficient: 1.89
Solvent content (%): 34.92
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: 2015-09-30
Structure of ULK1 bound to an inhibitor (PDB entry 4WNO)
Macromolecule: Serine/threonine-protein kinase ULK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 287 residues
Sequence: GGGSMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1784
R free: 0.2076
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 1.55 M sodium malonate pH 7.0,  0.35 M sodium malonate pH 5.0
Matthews coefficient: 2
Solvent content (%): 38.64
Ligand: N~2~-(4-aminophenyl)-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)quinazoline-2,4-diamine (3RF)
Ligand formula: C20 H19 N7
Ligand molecular weight: 357.412
Ligand SMILES: c1ccc2c(c1)c(nc(n2)Nc3ccc(cc3)N)Nc4cc([nH]n4)C5CC5
Ligand InChI: InChI=1S/C20H19N7/c21-13-7-9-14(10-8-13)22-20-23-16-4-2-1-3-15(16)19(25-20)24-18-11-17(26-27-18)12-5-6-12/h1-4,7-12H,5-6,21H2,(H3,22,23,24,25,26,27)
Release date: 2015-01-14
Tryptophan 5-hydroxylase in complex with inhibitor (3~{S})-8-[2-azanyl-6-[(1~{R})-1-(4-chloranyl-2-phenyl-phenyl)-2,2,2-tris(fluoranyl)ethoxy]pyrimidin-4-yl]-2,8-diazaspiro[4.5]decane-3-carboxylic acid (PDB entry 5L01)
Macromolecule: Tryptophan 5-hydroxylase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.4
Sequence length: 444 residues
Sequence: MIEDNKENKDHSLERGRASLIFSLKNEVGGLIKALKIFQEKHVNLLHIESRKSKRRNSEFEIFVDCDINREQLNDIFHLLKSHTNVLSVNLPDNFTLKEDGMETVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKYNPYTRSIQILKDTKSITSAMNELQHDLDVVSDALAKVSRKPSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.16925
R free: 0.21421
Average B factor: 25.226
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.05M citrate/0.05 M Bis-tris Propane pH 7.6, 5% PEG 400
Matthews coefficient: 1.51
Solvent content (%): 18.76
Ligand: (3~{S})-8-[2-azanyl-6-[(1~{R})-1-(4-chloranyl-2-phenyl-phenyl)-2,2,2-tris(fluoranyl)ethoxy]pyrimidin-4-yl]-2,8-diazaspiro[4.5]decane-3-carboxylic acid (6Z4)
Ligand formula: C27 H27 Cl F3 N5 O3
Ligand molecular weight: 561.983
Ligand SMILES: c1ccc(cc1)c2cc(ccc2C(C(F)(F)F)Oc3cc(nc(n3)N)N4CCC5(CC4)CC(NC5)C(=O)O)Cl
Ligand InChI: InChI=1S/C27H27ClF3N5O3/c28-17-6-7-18(19(12-17)16-4-2-1-3-5-16)23(27(29,30)31)39-22-13-21(34-25(32)35-22)36-10-8-26(9-11-36)14-20(24(37)38)33-15-26/h1-7,12-13,20,23,33H,8-11,14-15H2,(H,37,38)(H2,32,34,35)/t20-,23+/m0/s1
Release date: 2017-01-25
Crystal structure of the Fyn SH3 domain L112V-S114N-S115T-E129Q at pH 4.0 (PDB entry 7A2V)
Macromolecule: Tyrosine-protein kinase Fyn
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 60 residues
Sequence: GVTLFVALYDYEARTEDDLSFHKGEKFQIVNNTEGDWWEARSLTTGQTGYIPSNYVAPVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.2111
R free: 0.2195
Average B factor: 33.253
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4
Crystallization temperature (K): 298
Crystal growth procedure: 1.5 M ammonium sulfate, 0.1 sodium acetate
Matthews coefficient: 2.57
Solvent content (%): 52.17
Release date: 2021-08-25
Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming 8-oxo-dGTP (PDB entry 4XA5)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 325 residues
Sequence: NHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.19903
R free: 0.22725
Average B factor: 41.509
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 0.1 M sodium cacodylate trihydrate pH 7.4 and 1.9 M sodium acetate trihydrate
Matthews coefficient: 2.96
Solvent content (%): 58.46
Ligand: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (8DG)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(27-5)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
Release date: 2016-02-10
DDR1, 2-[3-(2-pyridin-3-ylethynyl)phenyl]-N-[3-(trifluoromethyl)phenyl]acetamide, 1.601A, P212121, Rfree=22.6% (PDB entry 5SAW)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.601
R work: 0.1994
R free: 0.226
Average B factor: 22.7854
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 9.2 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed with reservoir consisting of 0.1M MES/NaOH pH 6.5, 0.2M KI, 25% PEG 4000
Matthews coefficient: 2.34
Solvent content (%): 47.33
Ligand: 2-{3-[(pyridin-3-yl)ethynyl]phenyl}-N-[3-(trifluoromethyl)phenyl]acetamide (1IM)
Ligand formula: C22 H15 F3 N2 O
Ligand molecular weight: 380.363
Ligand SMILES: c1cc(cc(c1)C#Cc2cccnc2)CC(=O)Nc3cccc(c3)C(F)(F)F
Ligand InChI: InChI=1S/C22H15F3N2O/c23-22(24,25)19-7-2-8-20(14-19)27-21(28)13-18-5-1-4-16(12-18)9-10-17-6-3-11-26-15-17/h1-8,11-12,14-15H,13H2,(H,27,28)
Release date: 2022-06-29
Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors (PDB entry 5OWC)
Macromolecule: Group 10 secretory phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 122 residues
Sequence: GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1827
R free: 0.2208
Average B factor: 28.331
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 37-45% PEG400
0.1M bis-Tris pH 5.6-5.9
Matthews coefficient: 2.3
Solvent content (%): 46.58
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2018-08-01
Binary complex crystal structure of DNA polymerase Beta with A:G mismatch at the primer terminus (PDB entry 5J0Q)
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
R work: 0.2069
R free: 0.2612
Average B factor: 24.2186
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.44
Solvent content (%): 49.56
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-10-26
Human glucokinase in complex with novel pyrazole activator. (PDB entry 5V4X)
Macromolecule: Glucokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.2
Sequence length: 458 residues
Sequence: MKPMPLTLVEQILAEFQLQEEDLKKVMRRMQKEMDRGLRLETHEEASVKMLPTYVRSTPEGSEVGDFLSLDLGGTNFRVMLVKVGEGEEGQWSVKTKHQMYSIPEDAMTGTAEMLFDYISECISDFLDKHQMKHKKLPLGFTFSFPVRHEDIDKGILLNWTKGFKASGAEGNNVVGLLRDAIKRRGDFEMDVVAMVNDTVATMISCYYEDHQCEVGMIVGTGCNACYMEEMQNVELVEGDEGRMCVNTEWGAFGDSGELDEFLLEYDRLVDESSANPGQQLYEKLIGGKYMGELVRLVLLRLVDENLLFHGEASEQLRTRGAFETRFVSQVESDTGDRKQIYNILSTLGLRPSTTDCDIVRRACESVSTRAAHMCSAGLAGVINRMRESRSEDVMRITVGVDGSVYKLHPSFKERFHASVRRLTPSCEITFIESEEGSGRGAALVSAVACKKACMLGQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.1946
R free: 0.2503
Average B factor: 42.197
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 15% PEG3350, 200 mM ammonium iodide, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 2.22
Solvent content (%): 44.59
Ligand: (2S)-3-cyclohexyl-2-[4-(cyclopentylsulfonyl)-2-oxopyridin-1(2H)-yl]-N-(1,3-thiazol-2-yl)propanamide (8WJ)
Ligand formula: C22 H29 N3 O4 S2
Ligand molecular weight: 463.613
Ligand SMILES: c1csc(n1)NC(=O)C(CC2CCCCC2)N3C=CC(=CC3=O)S(=O)(=O)C4CCCC4
Ligand InChI: InChI=1S/C22H29N3O4S2/c26-20-15-18(31(28,29)17-8-4-5-9-17)10-12-25(20)19(14-16-6-2-1-3-7-16)21(27)24-22-23-11-13-30-22/h10-13,15-17,19H,1-9,14H2,(H,23,24,27)/t19-/m0/s1
Release date: 2017-05-31
Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated triazole-linked carboxylate zinc-chelator water-soluble inhibitor (DC28). (PDB entry 5I4O)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.21
R free: 0.249
Average B factor: 30
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Protein-ligand: 465 micro-M hMMP12 F171D E219Q, 0.020 M acetohydroxamic acid,  10% DMSO, 0.5 milli-M inhibitor (DC28).
Precipitant: 40.5% PEG4K,  10% dioxane, 2% ethylene glycol, 0.18 M imidazole piperidine, pH 8.5.
Cryoprotectant:40% cryomix CM12: (,25 % diethylene glycol + 12.5 % glycerol + 25 % 1,2-propanediol + 12.5 % 1,4-dioxane), 25% PEG 6K, 0.1 M TRIS HCl, pH 8.0.
Matthews coefficient: 2.22
Solvent content (%): 44.54
Ligand: N-({1-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1H-1,2,3-triazol-4-yl}methyl)-N-[([1,1'-biphenyl]-4-yl)sulfonyl]-D-valine (V28)
Ligand formula: C28 H35 N5 O9 S
Ligand molecular weight: 617.671
Ligand SMILES: CC(C)C(C(=O)O)N(Cc1cn(nn1)C2C(C(C(C(O2)CO)O)O)NC(=O)C)S(=O)(=O)c3ccc(cc3)c4ccccc4
Ligand InChI: InChI=1S/C28H35N5O9S/c1-16(2)24(28(38)39)33(43(40,41)21-11-9-19(10-12-21)18-7-5-4-6-8-18)14-20-13-32(31-30-20)27-23(29-17(3)35)26(37)25(36)22(15-34)42-27/h4-13,16,22-27,34,36-37H,14-15H2,1-3H3,(H,29,35)(H,38,39)/t22-,23-,24-,25-,26-,27-/m1/s1
Release date: 2016-07-06
Human CD73 (ecto 5'-nucleotidase) in complex with compound 12 (PDB entry 7JV9)
Macromolecule: 5'-nucleotidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.5
Sequence length: 525 residues
Sequence: SMWELTILHTNDVHSRLEQTSEDSSKCVDASRCMGGVARLFTKVQQIRRAEPNVLLLDAGDQYQGTIWFTVYKGAEVAHFMNALRYDAMALGNHEFDNGVEGLIEPLLKEAKFPILSANIKAKGPLASQISGLYLPYKVLPVGDEVVGIVGYTSKETPFLSNPGTNLVFEDEITALQPEVDKLKTLNVNKIIALGHSGFEMDKLIAQKVRGVDVVVGGHSNTFLYTGNPPSKEVPAGKYPFIVTSDDGRKVPVVQAYAFGKYLGYLKIEFDERGNVISSHGNPILLNSSIPEDPSIKADINKWRIKLDDYSTQELGKTIVYLDGSSQSCRFRECNMGNLICDAMINNNLRHTDEMFWNHVSMCILNGGGIRSPIDERNDGTITWENLAAVLPFGGTFDLVQLKGSTLKKAFEHSVHRYGQSTGEFLQVGGIHVVYDLSRKPGDRVVKLDVLCTKCRVPSYDPLKMDEVYKVILPNFLANGGDGFQMIKDELLRHDSGDQDINVVSTYISKMKVIYPAVEGRIKFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2092
R free: 0.2789
Average B factor: 57.627
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.25
Crystallization temperature (K): 277.15
Crystal growth procedure: 12.50 %w/v PEG 1500, 0.10M SPG (Succinic Acid, Sodium Dihydrogen Phosphate and Glycine) pH=4.25
Matthews coefficient: 2.53
Solvent content (%): 51.39
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: 2020-09-23
The Crystal Structure of Parkinson disease protein 7 (DJ-1) from Biortus (PDB entry 7C62)
Macromolecule: Protein/nucleic acid deglycase DJ-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.2
Sequence length: 206 residues
Sequence: MGGSHHHHHHENLYFQGMASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLEDAKKEGPYDVVVLPGGNLGAQNLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGFGSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAAQVKAPLVLKD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.027
R work: 0.152
R free: 0.1736
Average B factor: 27.223
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.1 M DL-Malic acid pH 7.0
Matthews coefficient: 2.74
Solvent content (%): 59.28
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: 2020-07-08
Crystal structure of wild type MNK2 in complex with inhibitor (PDB entry 6JLR)
Macromolecule: MAP kinase-interacting serine/threonine-protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 316 residues
Sequence: GSTDSFSGRFEDVYQLQEDVLGEGAHARVQTCINLITSQEYAVKIIEKQPGHIRSRVFREVEMLYQCQGHRNVLELIEFFEEEDRFYLVFEKMRGGSILSHIHKRRHFNELEASVVVQDVASALDFLHNKGIAHRDLKPENILCEHPNQVSPVKICDFDLGSGIKLNGDCSPISTPELLTPCGSAEYMAPEVVEAFSEEASIYDKRCDLWSLGVILYILLSGYPPFVGRCGSDCGWDRGEACPACQNMLFESIQEGKYEFPDKDWAHISCAAKDLISKLLVRDAKQRLSAAQVLQHPWVQGCAPENTLPTPMVLQR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.901
R work: 0.2973
R free: 0.3514
Average B factor: 86.4006
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.7
Crystallization temperature (K): 293
Crystal growth procedure: 23% polyacrylic acid 5100, 2% 2-methyl-2,4-pentane diol, 100mM Hepes pH 7.7
Matthews coefficient: 3.23
Solvent content (%): 61.92
Ligand: 4-[5-(1-methylpyrazol-4-yl)pyridin-3-yl]benzamide (BV9)
Ligand formula: C16 H14 N4 O
Ligand molecular weight: 278.309
Ligand SMILES: Cn1cc(cn1)c2cc(cnc2)c3ccc(cc3)C(=O)N
Ligand InChI: InChI=1S/C16H14N4O/c1-20-10-15(9-19-20)14-6-13(7-18-8-14)11-2-4-12(5-3-11)16(17)21/h2-10H,1H3,(H2,17,21)
Release date: 2020-02-12
H-Ras mutant L120A bound to GMP-PNP at 100K (PDB entry 5WDQ)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: FQGHMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDAAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1402
R free: 0.15
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 17% PEG8000, 200 mM calcium acetate, 100 mM MES/NaOH, pH 6.0
Matthews coefficient: 2.57
Solvent content (%): 52.08
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: 2017-07-19
Crystal structure of the WWP1 HECT domain in complex with H302, a Helicon Polypeptide (PDB entry 8EI4)
Macromolecule: NEDD4-like E3 ubiquitin-protein ligase WWP1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.26
Sequence length: 376 residues
Sequence: GSHMGFRWKLAHFRYLCQSNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRRRLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFIAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDMEILGKVTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQEQTKAFLDGFNEVVPLQWLQYFDEKELEVMLCGMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETDNEVRMRLLQFVTGTCRLPLGGFAELMGSNGPQKFCIEKVGKDTWLPRSHTCFNRLDLPPYKSYEQLKEKLLFAIEETE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.2192
R free: 0.2808
Average B factor: 45.5991
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Sodium acetate, 0.1 M Sodium citrate pH 5.5, 5% w/v PEG 4000
Matthews coefficient: 2.56
Solvent content (%): 51.97
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: 2023-10-25
Carbonic Anhydrase 2 in Complex with Steriod_Sulphamoyl AKI33 (PDB entry 8OMP)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.16141
R free: 0.1845
Average B factor: 12.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.08
Solvent content (%): 40.98
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: 2024-04-10
Human pancreatic alpha amylase in complex with peptide inhibitor piHA-L5(d10Y) (PDB entry 5VA9)
Macromolecule: Pancreatic alpha-amylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.1
Sequence length: 496 residues
Sequence: QYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.1958
R free: 0.2297
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: MPD 54%, 0.1 M sodium cacodylate.
Matthews coefficient: 2.63
Solvent content (%): 53.18
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: 2018-03-28