satarupa22/MacromolecularLigandDB huggingface dataset:
Human Mtr4 helicase in complex with ZCCHC8-CTD (PDB entry 6C90)
Macromolecule: Exosome RNA helicase MTR4,Exosome RNA helicase MTR4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 734 residues
Sequence: SGDTDEPIFGKKPRIEESITEDLSLADLMPRVKVQSVETVEGCTHEVALPAEEDYLPLKPRVGKAAKEYPFILDAFQREAIQCVDNNQSVLVSAHTSAGKTVCAEYAIALALREKQRVIFTSPIKALSNQKYREMYEEFQDVGLMTGDVTINPTASCLVMTTEILRSMLYRGSEVMREVAWVIFDEIHYMRDSERGVVWEETIILLPDNVHYVFLSATIPNARQFAEWICHLHKQPCHVIYTDYRPTPLQHYIFPAGGDGLHLVVDENGDFREDNFNTAMQVLRDAGDLAKGDQKGRKGGTKGPSNVFKIVKMIMERNFQPVIIFSFSKKDCEAYALQMTKLDFNTDEEKKMVEEVFSNAIDCLSDEDKKLPQVEHVLPLLKRGIGIHHGGLLPILKETIEILFSEGLIKALFATETFAMGINMPARTVLFTNARKFDGKDFRWISSGEYIQMSGRAGRRGMDDRGIVILMVDEKMSPTIGKQLLKGSADPLNSAFHLTYNMVLNLLRVEEINPEYMLEKSFYQFQHYRAIPGSRTVLQMDELKCRKRVLRRLGFATSSDVIEMKGRVACEISSADELLLTEMMFNGLFNDLSAEQATALLSCFVFQENSSEMPKLTEQLAGPLRQMQECAKRIAKVSAEAKLEIDEETYLSSFKPHLMDVVYTWATGATFAHICKMTDVFEGSIIRCMRRLEELLRQMCQAAKAIGNTELENKFAEGITKIKRDIVFAASLYL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1903
R free: 0.2214
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium-potassium (L)-tartrate, 0.1 M Bis-Tris pH 6.5
Matthews coefficient: 3.59
Solvent content (%): 65.72
Ligand: L(+)-TARTARIC ACID (TLA)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m1/s1
Release date: 2018-05-30
Ligand-induced conformational change of Insulin-regulated aminopeptidase: insights on catalytic mechanism and active site plasticity. (PDB entry 5MJ6)
Macromolecule: Leucyl-cystinyl aminopeptidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.3
Sequence length: 881 residues
Sequence: ATNGKLFPWAQIRLPTAVVPLRYELSLHPNLTSMTFRGSVTISVQALQVTWNIILHSTGHNISRVTFMSAVSSQEKQAEILEYAYHGQIAIVAPEALLAGHNYTLKIEYSANISSSYYGFYGFSYTDESNEKKYFAATQFEPLAARSAFPCFDEPAFKATFIIKIIRDEQYTALSNMPKKSSVVLDDGLVQDEFSESVKMSTYLVAFIVGEMKNLSQDVNGTLVSIYAVPEKIGQVHYALETTVKLLEFFQNYFEIQYPLKKLDLVAIPDFEAGAMENWGLLTFREETLLYDSNTSSMADRKLVTKIIAHELAHQWFGNLVTMKWWNDLWLNEGFATFMEYFSLEKIFKELSSYEDFLDARFKTMKKDSLNSSHPISSSVQSSEQIEEMFDSLSYFKGSSLLLMLKTYLSEDVFQHAVVLYLHNHSYASIQSDDLWDSFNEVTNQTLDVKRMMKTWTLQKGFPLVTVQKKGKELFIQQERFFLNMKPEIQPSDTSYLWHIPLSYVTEGRNYSKYQSVSLLDKKSGVINLTEEVLWVKVNINMNGYYIVHYADDDWEALIHQLKINPYVLSDKDRANLINNIFELAGLGKVPLKRAFDLINYLGNENHTAPITEALFQTDLIYNLLEKLGYMDLASRLVTRVFKLLQNQIQQQTWTDEGTPSMRELRSALLEFACTHNLGNCSTTAMKLFDDWMASNGTQSLPTDVMTTVFKVGAKTDKGWSFLLGKYISIGSEAEKNKILEALASSEDVRKLYWLMKSSLNGDNFRTQKLSFIIRTVGRHFPGHLLAWDFVKENWNKLVQKFPLGSYTIQNIVAGSTYLFSTKTHLSEVQAFFENQSEATFRLRCVQEALEVIQLNIQWMEKNLKSLTWWLRTETSQVAPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.1738
R free: 0.2292
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 18.8% (w/v) PEG of mean MW 20000, 37.6% (v/v) PEG monomethyl ether of mean MW 500, 50.2 mM Bicine, 43.8 mM Trizma base (pH of buffer mixture: 8.5) and 0.282 M each of the following halogens: Sodium fluoride, Sodium bromide and Sodium iodide
Matthews coefficient: 2.39
Solvent content (%): 58.98
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2017-04-05
The ATAD2 bromodomain in complex with compound 2 (PDB entry 6EPU)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.192
R free: 0.2184
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5
Matthews coefficient: 4.06
Solvent content (%): 69.68
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: 2018-10-31
human cGAS core domain (K427E/K428E) bound with RU-521 (PDB entry 6O47)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 372 residues
Sequence: SILVRRDAAPGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDEEHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.196
R work: 0.1815
R free: 0.2214
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 0.064 M sodium citrate 7.0, 0.1 M HEPES, pH 7.0, 10% PEG5000MME
Matthews coefficient: 2.87
Solvent content (%): 57.19
Ligand: CITRIC ACID (CIT)
Ligand formula: C6 H8 O7
Ligand molecular weight: 192.124
Ligand SMILES: C(C(=O)O)C(CC(=O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C6H8O7/c7-3(8)1-6(13,5(11)12)2-4(9)10/h13H,1-2H2,(H,7,8)(H,9,10)(H,11,12)
Release date: 2019-05-29
Protein Tyrosine Phosphatase 1B (PDB entry 7LFO)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 329 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHNLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.2004
R free: 0.243
Average B factor: 47.258
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 140 g/L PEG8000, 100 mM HEPES, 200 mM magnesium acetate, pH 7.5
Matthews coefficient: 3.04
Solvent content (%): 59.59
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: 2021-05-26
EGFR kinase domain (L858R/V948R) in complex with 2-[4-(difluoromethyl)-6-[2-[4-[[4-(hydroxymethyl)-1-piperidyl]methyl]phenyl]ethynyl]-7-methyl-indazol-2-yl]-2-spiro[6,7-dihydropyrrolo[1,2-c]imidazole-5,1'-cyclopropane]-1-yl-N-thiazol-2-yl-acetamide (PDB entry 8A2D)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 326 residues
Sequence: GSMNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.11
R work: 0.1632
R free: 0.1788
Average B factor: 15.73
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG Smear High, 0.1M MES
Matthews coefficient: 1.8
Solvent content (%): 31.79
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: 2022-10-19
Crystal structure of CREBBP bromodomain complexed with DK19 (PDB entry 5MPK)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1828
R free: 0.2391
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES-Na, pH7.5, 0.2 M MgCl2, 25% P3350
Matthews coefficient: 2.09
Solvent content (%): 41.15
Ligand: ~{N}-(5-ethanoyl-2-ethoxy-phenyl)-3-(2~{H}-1,2,3,4-tetrazol-5-yl)-5-(1,3-thiazol-4-yl)benzamide (0BC)
Ligand formula: C21 H18 N6 O3 S
Ligand molecular weight: 434.471
Ligand SMILES: CCOc1ccc(cc1NC(=O)c2cc(cc(c2)c3n[nH]nn3)c4cscn4)C(=O)C
Ligand InChI: InChI=1S/C21H18N6O3S/c1-3-30-19-5-4-13(12(2)28)9-17(19)23-21(29)16-7-14(18-10-31-11-22-18)6-15(8-16)20-24-26-27-25-20/h4-11H,3H2,1-2H3,(H,23,29)(H,24,25,26,27)
Release date: 2018-01-17
Human Angiogenin mutant-S28AT36AS37A (PDB entry 7PNR)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 121 residues
Sequence: QDNSRYTHFLTQHYDAKPQGRDDRYCEAIMRRRGLAAPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.18981
R free: 0.20103
Average B factor: 27.906
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: Malic acid/NaOH pH 7.0, PEG 3350
Matthews coefficient: 2.29
Solvent content (%): 46.21
Release date: 2021-09-29
EGFR kinase in complex with a macrocyclic inhibitor (PDB entry 7U99)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSTSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.187
R free: 0.2139
Average B factor: 69.706
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 6.5, 1.1 M Sodium Citrate
Matthews coefficient: 3.41
Solvent content (%): 63.95
Ligand: 19-chloro-22-methoxy-8,9,11,12,14,15-hexahydro-21H-4,6-ethenopyrimido[5,4-m][1,4,7,10,15]benzotetraoxazacycloheptadecine (M0R)
Ligand formula: C21 H22 Cl N3 O5
Ligand molecular weight: 431.869
Ligand SMILES: COc1cc2c3cc1OCCOCCOCCOc4ccc(cc4Nc3ncn2)Cl
Ligand InChI: InChI=1S/C21H22ClN3O5/c1-26-19-12-16-15-11-20(19)30-9-7-28-5-4-27-6-8-29-18-3-2-14(22)10-17(18)25-21(15)24-13-23-16/h2-3,10-13H,4-9H2,1H3,(H,23,24,25)
Release date: 2022-11-23
Crystal structure of BACE complex with BMC010 (PDB entry 5QD3)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.164
R free: 0.2
Average B factor: 47.78
Crystallization method: hanging drop
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE IN WATER. PROTEIN STOCK WAS
BACE MUT46B BATCH XVI 7.0MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 6-FOLD EXCESS OF BMC010 ADDED FROM A 50MM
STOCK SOLUTION IN 90% DMSO-D6 (1.7% DMSO IN DROP). A SOLUTION CONTAINING 1.2M AMMONIUM SULFATE, 25% GLYCEROL, 1MM BMC010
AND 1.8% DMSO WAS USED AS CRYO-PROTECTANT.
Matthews coefficient: 3.16
Solvent content (%): 61.08
Ligand: (10R,12S)-12-[(1R)-1-hydroxy-2-({[3-(propan-2-yl)phenyl]methyl}amino)ethyl]-17-(methoxymethyl)-10-methyl-2,13-diazabicyclo[13.3.1]nonadeca-1(19),15,17-trien-14-one (E6M)
Ligand formula: C32 H49 N3 O3
Ligand molecular weight: 523.75
Ligand SMILES: CC1CCCCCCCNc2cc(cc(c2)C(=O)NC(C1)C(CNCc3cccc(c3)C(C)C)O)COC
Ligand InChI: InChI=1S/C32H49N3O3/c1-23(2)27-13-10-12-25(16-27)20-33-21-31(36)30-15-24(3)11-8-6-5-7-9-14-34-29-18-26(22-38-4)17-28(19-29)32(37)35-30/h10,12-13,16-19,23-24,30-31,33-34,36H,5-9,11,14-15,20-22H2,1-4H3,(H,35,37)/t24-,30+,31-/m1/s1
Release date: 2020-06-03
KRasG12C ligand complex (PDB entry 8B78)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 168 residues
Sequence: GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVDDAFYTLVREIRKHK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.11
R work: 0.2236
R free: 0.2357
Average B factor: 20.835
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350
LITHIUM SULFATE
Matthews coefficient: 2.75
Solvent content (%): 55.23
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: 2023-07-12
Tankyrase 2 in complex with an inhibitor (PDB entry 8B6M)
Macromolecule: Poly [ADP-ribose] polymerase tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 171 residues
Sequence: SMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1849
R free: 0.2194
Average B factor: 27.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 100 mM Tris, 22% w/v PEG3350, 200 mM Li2SO4, 250 mM NaCl, 20% v/v glycerol
Matthews coefficient: 2.65
Solvent content (%): 53.5
Ligand: ~{N}-(2-methoxyphenyl)-4-[[2-(4-oxidanylidene-3~{H}-quinazolin-2-yl)ethyl-(thiophen-2-ylmethyl)carbamoyl]amino]benzamide (OY6)
Ligand formula: C30 H27 N5 O4 S
Ligand molecular weight: 553.631
Ligand SMILES: COc1ccccc1NC(=O)c2ccc(cc2)NC(=O)N(CCC3=Nc4ccccc4C(=O)N3)Cc5cccs5
Ligand InChI: InChI=1S/C30H27N5O4S/c1-39-26-11-5-4-10-25(26)33-28(36)20-12-14-21(15-13-20)31-30(38)35(19-22-7-6-18-40-22)17-16-27-32-24-9-3-2-8-23(24)29(37)34-27/h2-15,18H,16-17,19H2,1H3,(H,31,38)(H,33,36)(H,32,34,37)
Release date: 2023-10-11
Crystal structure of human LTA4H mutant D375N in open conformation (crystal form I) (PDB entry 5NIA)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 617 residues
Sequence: MHHHHHHPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPNVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.764
R work: 0.1801
R free: 0.2074
Average B factor: 47.94
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 8% (w/v) PEG 20 000, 15% (w/v) PEG MME 550, 100 mM Hepes/MOPS pH 7.7-8.0, 15 mM CaCl2, 15 mM MgCl2
Matthews coefficient: 2.46
Solvent content (%): 50
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: 2017-08-23
Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 5,6,7-tribromo-1H-imidazo[4,5-b]pyridine (PDB entry 7A2H)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.01
R work: 0.1426
R free: 0.1495
Average B factor: 17.38
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Reservoir composition: 28 % (w/v) PEG6000, 0.9 M LiCl, 0.1 M, Tris/HCl, pH 8.5; drop composition prior to equilibration: 0.01 ml reservoir solution + 0.02 ml CK2alpha' (mutant Cys336Ser)/inhibitor MB002 mixture (0.180 ml 6 mg/ml CK2alpha'Cys336Ser, 0.5 M NaCl, 25 mM Tris/HCl, pH 8.5, mixed and pre-equilibrated with 0.02 ml 10 mM MB002 in dimethyl sulfoxide); the initial inhibitor MB002 was replaced by the inhibitor 5,6,7-tribromo-1H-imidazo[4,5-b]pyridine by extensive crystal soaking.
Matthews coefficient: 2.67
Solvent content (%): 53.88
Ligand: 5,6,7-tris(bromanyl)-1~{H}-imidazo[4,5-b]pyridine (QX2)
Ligand formula: C6 H2 Br3 N3
Ligand molecular weight: 355.812
Ligand SMILES: c1[nH]c2c(c(c(nc2n1)Br)Br)Br
Ligand InChI: InChI=1S/C6H2Br3N3/c7-2-3(8)5(9)12-6-4(2)10-1-11-6/h1H,(H,10,11,12)
Release date: 2020-12-09
Human Aldose Reductase Mutant L301A in Complex with a Ligand with an IDD Structure (3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid) (PDB entry 6T7Q)
Macromolecule: Aldo-keto reductase family 1 member B1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.300
Sequence length: 316 residues
Sequence: MASRILLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALASCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.01
R work: 0.1177
R free: 0.1322
Average B factor: 11.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Di-Ammoniumhydrogen citrate pH 5.0: 15 mg/mL hAR, 5.2 mg/mL DTT, 0.7 mg/mL NADP+, 5% (w/v) PEG 6000
Reservoir: 120 mM Di-Ammoniumhydrogen citrate pH 5.0, 20% (w/v) PEG 6000
Soaking-buffer: 120 mM Di-Ammoniumhydrogen citrate pH 5.0, 25% (w/v) PEG 6000
Matthews coefficient: 2.18
Solvent content (%): 43.67
Ligand: 3-({[2-(carboxymethoxy)-4-fluorobenzoyl]amino}methyl)benzoic acid (4G7)
Ligand formula: C17 H14 F N O6
Ligand molecular weight: 347.295
Ligand SMILES: c1cc(cc(c1)C(=O)O)CNC(=O)c2ccc(cc2OCC(=O)O)F
Ligand InChI: InChI=1S/C17H14FNO6/c18-12-4-5-13(14(7-12)25-9-15(20)21)16(22)19-8-10-2-1-3-11(6-10)17(23)24/h1-7H,8-9H2,(H,19,22)(H,20,21)(H,23,24)
Release date: 2020-11-18
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2064898339 (PDB entry 5RW3)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.37
R work: 0.1707
R free: 0.196
Average B factor: 18.421
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.62
Ligand: 2-(4-methylphenyl)-N-{[(2S)-oxolan-2-yl]methyl}acetamide (WLY)
Ligand formula: C14 H19 N O2
Ligand molecular weight: 233.306
Ligand SMILES: Cc1ccc(cc1)CC(=O)NCC2CCCO2
Ligand InChI: InChI=1S/C14H19NO2/c1-11-4-6-12(7-5-11)9-14(16)15-10-13-3-2-8-17-13/h4-7,13H,2-3,8-10H2,1H3,(H,15,16)/t13-/m0/s1
Release date: 2020-11-11
Crystal structure of tumor related RhoA mutant A161V in complex with GDP (PDB entry 8FPW)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 183 residues
Sequence: GSMAAIRKKLVIVGDGACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSVKTKDGVREVFEMATRAALQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1781
R free: 0.2079
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 20-24% PEG8K, 15% Dioxane, 0.1M Tris pH8.0
Matthews coefficient: 2.31
Solvent content (%): 46.85
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2024-06-05