satarupa22/MacromolecularLigandDB huggingface dataset:
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with OX-220 (PDB entry 5QGO)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.82
R work: 0.2004
R free: 0.2235
Average B factor: 40.04
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.32
Solvent content (%): 71.54
Ligand: (3aR,4R,6R,7R,8aR)-6-phenyloctahydro-1H-3a,7-epiminocyclohepta[c]pyrrol-4-ol (H4A)
Ligand formula: C15 H20 N2 O
Ligand molecular weight: 244.332
Ligand SMILES: c1ccc(cc1)C2CC(C34CNCC3CC2N4)O
Ligand InChI: InChI=1S/C15H20N2O/c18-14-7-12(10-4-2-1-3-5-10)13-6-11-8-16-9-15(11,14)17-13/h1-5,11-14,16-18H,6-9H2/t11-,12-,13-,14-,15+/m1/s1
Release date: 2019-03-27
Co-crystal structure of the tandem CNB (CNB-A/B) domains of human PKG I beta with cGMP (PDB entry 4Z07)
Macromolecule: cGMP-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.12
Sequence length: 262 residues
Sequence: GSSHVTLPFYPKSPQSKDLIKEAILDNDFMKNLELSQIQEIVDCMYPVEYGKDSCIIKEGDVGSLVYVMEDGKVEVTKEGVKLCTMGPGKVFGELAILYNCTRTATVKTLVNVKLWAIDRQCFQTIMMRTGLIKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGTVNVTREDSPSEDPVFLRTLGKGDWFGEKALQGEDVRTANVIAAEAVTCLVIDRDSFKHLIGGLDDVSNKAY
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1623
R free: 0.2237
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 0.2 M ammonium sulfate, 17.5% PEG 8000 (w/v), 10% Isopropanol, 0.1 M HEPES, pH 8.0
Matthews coefficient: 2.84
Solvent content (%): 56.71
Ligand: CYCLIC GUANOSINE MONOPHOSPHATE (PCG)
Ligand formula: C10 H12 N5 O7 P
Ligand molecular weight: 345.205
Ligand SMILES: c1nc2c(n1C3C(C4C(O3)COP(=O)(O4)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H12N5O7P/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6-3(21-9)1-20-23(18,19)22-6/h2-3,5-6,9,16H,1H2,(H,18,19)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
Release date: 2016-04-13
Crystal structure of human tankyrase 2 in complex with OD336 (PDB entry 5NOB)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.20158
R free: 0.23657
Average B factor: 27.764
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M TMAO, 0.1M Tris, 20% PEG 2000 MME
Matthews coefficient: 2.25
Solvent content (%): 45.27
Ligand: 1-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]cyclobutyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile (92T)
Ligand formula: C24 H17 Cl N8 O
Ligand molecular weight: 468.898
Ligand SMILES: c1ccc(c(c1)n2c(nnc2C3CC(C3)N4c5ccc(cc5NC4=O)C#N)c6ccncn6)Cl
Ligand InChI: InChI=1S/C24H17ClN8O/c25-17-3-1-2-4-20(17)33-22(30-31-23(33)18-7-8-27-13-28-18)15-10-16(11-15)32-21-6-5-14(12-26)9-19(21)29-24(32)34/h1-9,13,15-16H,10-11H2,(H,29,34)/t15-,16-
Release date: 2017-11-29
RENIN IN COMPLEXED WITH 4-methoxy-3-(3-methoxypropoxy)-N-{[(3S,4S)-4-{[(4-methylphenyl)sulfonyl]amino}pyrrolidin-3-yl]methyl}-N-(propan-2-yl)benzamide INHIBITOR (PDB entry 4RYC)
Macromolecule: Renin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.15
Sequence length: 340 residues
Sequence: LTLGNTTSSVILTNYMDTQYYGEIGIGTPPQTFKVVFDTGSSNVWVPSSKCSRLYTACVYHKLFDASDSSSYKHNGTELTLRYSTGTVSGFLSQDIITVGGITVTQMFGEVTEMPALPFMLAEFDGVVGMGFIEQAIGRVTPIFDNIISQGVLKEDVFSFYYNRDSENSQSLGGQIVLGGSDPQHYEGNFHYINLIKTGVWQIQMKGVSVGSSTLLCEDGCLALVDTGASYISGSTSSIEKLMEALGAKKRLFDYVVKCNEGPTLPDISFHLGGKEYTLTSADYVFQESYSSKKLCTLAIHAMDIPPPTGPTWALGATFIRKFYTEFDRRNNRIGFALAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.1905
R free: 0.2289
Average B factor: 51.7
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: HANGING DROP, VAPOR DIFFUSION, 20 DEG C, 1 UL PROTEIN + 1 UL RESERVOIR; PROTEIN SOLUTION: 31.7 MG/ML RENIN, 12.5 MM TRIS PH 8, 25 MM NACL; RESERVOIR SOLUTION: 21% PEG4000, 50 MM NACITRATE PH 4.5, 600 MM NACL; SOAKING: DROP PLUS 2.5 UL RESERVOIR SOLUTION PLUS 10 MM COMPOUND AND 10% DMSO FOR 30 MIN; CRYO: SOAKING SOLUTION PLUS 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 3.18
Solvent content (%): 61.35
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: 2015-03-25
human cGAS catalytic domain bound with cGAMP (PDB entry 6MJX)
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): 2.6
R work: 0.2212
R free: 0.265
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Bicine 8.5, 10% PEG6000, final PH 9.0
Matthews coefficient: 2.23
Solvent content (%): 44.73
Ligand: cGAMP (1SY)
Ligand formula: C20 H24 N10 O13 P2
Ligand molecular weight: 674.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(C(COP(=O)(O4)O)OC5n6cnc7c6NC(=NC7=O)N)O)O)O)N
Ligand InChI: InChI=1S/C20H24N10O13P2/c21-14-8-15(24-3-23-14)29(4-25-8)18-11(32)12-7(41-18)2-39-45(36,37)43-13-10(31)6(1-38-44(34,35)42-12)40-19(13)30-5-26-9-16(30)27-20(22)28-17(9)33/h3-7,10-13,18-19,31-32H,1-2H2,(H,34,35)(H,36,37)(H2,21,23,24)(H3,22,27,28,33)/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
Release date: 2019-05-29
Crystal Structure Analysis of human PRPK complex with a compound (PDB entry 7SZA)
Macromolecule: EKC/KEOPS complex subunit TP53RK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6
Sequence length: 255 residues
Sequence: GPMAAARATTPADGEEPAPEAEALAAARERSSRFLSGLELVKQGAEARVFRGRFQGRAAVIKHRFPKGYRHPALEARLGRRRTVQEARALLRCRRAGISAPVVFFVDYASNCLYMEEIEGSVTVRDYIQSTMETEKTPQGLSNLAKTIGQVLARMHDEDLIHGDLTTSNMLLKPPLEQLNIVLIDFGLSFISALPEDKGVDLYVLEKAFLSTHPNTETVFEAFLKSYSTSSKKARPVLKKLDEVRLRGRKRSMVG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1728
R free: 0.2163
Average B factor: 36.4617
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.2
Crystallization temperature (K): 300
Crystal growth procedure: 100mM Sodium citrate pH 5.2, 12.8% PEG8000, 10mM MgCl2, 10mM TCEP
Matthews coefficient: 2.26
Solvent content (%): 45.59
Ligand: 4-amino-2-[(3R)-2,6-dioxopiperidin-3-yl]-1H-isoindole-1,3(2H)-dione (DUI)
Ligand formula: C13 H11 N3 O4
Ligand molecular weight: 273.244
Ligand SMILES: c1cc2c(c(c1)N)C(=O)N(C2=O)C3CCC(=O)NC3=O
Ligand InChI: InChI=1S/C13H11N3O4/c14-7-3-1-2-6-10(7)13(20)16(12(6)19)8-4-5-9(17)15-11(8)18/h1-3,8H,4-5,14H2,(H,15,17,18)/t8-/m1/s1
Release date: 2023-01-25
Crystal structure of XIAP-BIR3 in complex with a cIAP1-selective SM (PDB entry 6EY2)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 146 residues
Sequence: HHHHHHSSGLVPRGSHMASMTGGQQMGRGSSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2351
R free: 0.28408
Average B factor: 71.01
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 10% PEG 400, 0.2 M MgCl2, 0.1M Hepes-Na
Matthews coefficient: 2.73
Solvent content (%): 54.95
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: 2018-08-08
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS040404c (PDB entry 5RAI)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1908
R free: 0.2176
Average B factor: 33.952
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.78
Solvent content (%): 55.75
Ligand: (1-methyl-5-phenyl-pyrazol-3-yl)methanol (S3M)
Ligand formula: C11 H12 N2 O
Ligand molecular weight: 188.226
Ligand SMILES: Cn1c(cc(n1)CO)c2ccccc2
Ligand InChI: InChI=1S/C11H12N2O/c1-13-11(7-10(8-14)12-13)9-5-3-2-4-6-9/h2-7,14H,8H2,1H3
Release date: 2020-04-22
Incomplete in crystallo incorporation by DNA Polymerase Lambda bound to blunt-ended DSB substrate and incoming dTTP (PDB entry 7M0A)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 346 residues
Sequence: GSAAAVLDKWVCAQPSSQKATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.169
R free: 0.1933
Average B factor: 26.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 80mM Na cacodylate pH 6.5, 0.16M calcium acetate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol
Matthews coefficient: 3
Solvent content (%): 59.1
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: 2022-03-16
Crystal structures of human E-NPP 1: bound to adenosine-5'-thio-monophosphate (PDB entry 6WEU)
Macromolecule: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.1
Sequence length: 925 residues
Sequence: MERDGCAGGGSRGGEGGRAPREGPAGNGRDRGRSHAAEAPGDPQAAASLLAPMDVGEEPLEKAARARTAKDPNTYKVLSLVLSVCVLTTILGCIFGLKPSCAKEVKSCKGRCFERTFGNCRCDAACVELGNCCLDYQETCIEPEHIWTCNKFRCGEKRLTRSLCACSDDCKDKGDCCINYSSVCQGEKSWVEEPCESINEPQCPAGFETPPTLLFSLDGFRAEYLHTWGGLLPVISKLKKCGTYTKNMRPVYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPEWYKGEPIWVTAKYQGLKSGTFFWPGSDVEINGIFPDIYKMYNGSVPFEERILAVLQWLQLPKDERPHFYTLYLEEPDSSGHSYGPVSSEVIKALQRVDGMVGMLMDGLKELNLHRCLNLILISDHGMEQGSCKKYIYLNKYLGDVKNIKVIYGPAARLRPSDVPDKYYSFNYEGIARNLSCREPNQHFKPYLKHFLPKRLHFAKSDRIEPLTFYLDPQWQLALNPSERKYCGSGFHGSDNVFSNMQALFVGYGPGFKHGIEADTFENIEVYNLMCDLLNLTPAPNNGTHGSLNHLLKNPVYTPKHPKEVHPLVQCPFTRNPRDNLGCSCNPSILPIEDFQTQFNLTVAEEKIIKHETLPYGRPRVLQKENTICLLSQHQFMSGYSQDILMPLWTSYTVDRNDSFSTEDFSNCLYQDFRIPLSPVHKCSFYKNNTKVSYGFLSPPQLNKNSSGIYSEALLTTNIVPMYQSFQVIWRYFHDTLLRKYAEERNGVNVVSGPVFDFDYDGRCDSLENLRQKRRVIRNQEILIPTHFFIVLTSCKDTSQTPLHCENLDTLAFILPHRTDNSESCVHGKHDSSWVEELLMLHRARITDVEHITGLSFYQQRKEPVSDILKLKTHLPTFSQED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.207
R free: 0.239
Average B factor: 60.145
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 7.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate
Matthews coefficient: 3.32
Solvent content (%): 62.9
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-09-09
Human MALT1(329-729) in complex with a chromane urea containing inhibitor (PDB entry 7AK1)
Macromolecule: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22
Sequence length: 404 residues
Sequence: GPGSDNKEQTTDQPLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSSLSEKRALTDPIQGTEYSAESLVRNLQWAKAHELPESMCLKFDCGVQIQLGFAAEFSNVMIIYTSIVYKPPEIIMCDAYVTDFPLDLDIDPKDANKGTPEETGSYLVSKDLPKHCLYTRLSSLQKLKEHLVFTVCLSYQYSGLEDTVEDKQEVNVGKPLIAKLDMHRGLGRKTCFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.507
R work: 0.1962
R free: 0.2651
Average B factor: 51.17
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 12.2 mg/ml, 25mM HEPES pH7.5, 50mM NaCL, 1mM TCEP
Matthews coefficient: 2.54
Solvent content (%): 51.64
Ligand: 1-(3-chloranyl-4-methoxy-phenyl)-3-[7-[(3~{S})-3-(methoxymethyl)morpholin-4-yl]-2-methyl-pyrazolo[1,5-a]pyrimidin-6-yl]urea (RJH)
Ligand formula: C21 H25 Cl N6 O4
Ligand molecular weight: 460.914
Ligand SMILES: Cc1cc2ncc(c(n2n1)N3CCOCC3COC)NC(=O)Nc4ccc(c(c4)Cl)OC
Ligand InChI: InChI=1S/C21H25ClN6O4/c1-13-8-19-23-10-17(25-21(29)24-14-4-5-18(31-3)16(22)9-14)20(28(19)26-13)27-6-7-32-12-15(27)11-30-2/h4-5,8-10,15H,6-7,11-12H2,1-3H3,(H2,24,25,29)/t15-/m0/s1
Release date: 2020-12-09
Structure of human ACE2 in complex with a fluorinated small molecule inhibitor (PDB entry 9FMM)
Macromolecule: Angiotensin-converting enzyme 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17.23
Sequence length: 730 residues
Sequence: STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKNQMILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRINDAFRLNDNSLEFLGIQPTLGPPNQPPVSHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2126
R free: 0.2651
Average B factor: 60.61
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium citrate pH 5.5, 20% w/v PEG 3000
Matthews coefficient: 2.49
Solvent content (%): 50.53
Ligand: (2~{S})-2-[[(2~{S})-3-[3-[(3-chloranyl-5-fluoranyl-phenyl)methyl]imidazol-4-yl]-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-4-methyl-pentanoic acid (A1IDX)
Ligand formula: C19 H23 Cl F N3 O4
Ligand molecular weight: 411.855
Ligand SMILES: CC(C)CC(C(=O)O)NC(Cc1cncn1Cc2cc(cc(c2)Cl)F)C(=O)O
Ligand InChI: InChI=1S/C19H23ClFN3O4/c1-11(2)3-16(18(25)26)23-17(19(27)28)7-15-8-22-10-24(15)9-12-4-13(20)6-14(21)5-12/h4-6,8,10-11,16-17,23H,3,7,9H2,1-2H3,(H,25,26)(H,27,28)/t16-,17-/m0/s1
Release date: 2024-07-17
17beta-HSD5 in complex with 3-pentyl-2-[(pyridin-2-ylmethyl)sulfanyl]-7-(pyrrolidin-1-ylcarbonyl)quinazolin-4(3H)-one (PDB entry 4XVE)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.64
Sequence length: 331 residues
Sequence: MDSKHQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEYLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.17912
R free: 0.20308
Average B factor: 14.869
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M sodium citrate, 0.4 M ammonium acetate, 2.5% (v/v) 2-methyl-2,4-pentanediol, 22-30% (w/v) PEG4000
Matthews coefficient: 2.18
Solvent content (%): 43.5
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2015-04-15
Crystal structure of SHP2_SH2-CagA EPIYA_C peptide complex (PDB entry 5X7B)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 220 residues
Sequence: MTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTR
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.2252
R free: 0.278
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 29%(w/v) PEG4000, 0.1 M Tris-HCl, 0.13 M sodium acetate
Matthews coefficient: 2.2
Solvent content (%): 43.99
Release date: 2017-09-13
Crystal structure of MMP9 in complex with inhibitor BE4. (PDB entry 6ESM)
Macromolecule: Matrix metalloproteinase-9,Matrix metalloproteinase-9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.35
Sequence length: 160 residues
Sequence: FEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.104
R work: 0.1557
R free: 0.1722
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Protein: human MMP9 E402Q  300 micro-M
Precipitant: 31.5% MPEG 5K; .14 M imidazole piperidine; pH 8.5
Cryoprotectant: 40% CM2 (25% di-ethylene glycol + 25% glycerol + 25% 1,2-propanediol), 10% PEG 10K, 200 milli-M NaCl, 100milli-M PCTP 50/50
Matthews coefficient: 2.08
Solvent content (%): 40.82
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: 2018-05-16
Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-[(4-benzylpiperazin-1-yl)methyl]-6-(2-chloro-4-methylphenyl)-1H-benzimidazole-4-carboxylic acid (PDB entry 7FUM)
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): 2.06
R work: 0.233
R free: 0.269
Average B factor: 87.78
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: 2.61
Solvent content (%): 52.82
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: 2024-02-21
Human Cyclophilin D in complex with N-(4-aminophenyl)-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide (PDB entry 7R2J)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.1401
R free: 0.1656
Average B factor: 11.65
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277.15
Crystal growth procedure: 15 % PEG 3350, 0.1M K2HPO4
Matthews coefficient: 1.9
Solvent content (%): 35.14
Ligand: N-(4-aminophenyl)-7-methyl-2-oxo-1H,2H-pyrazolo[1,5-a]pyrimidine-6-carboxamide (V0Z)
Ligand formula: C14 H13 N5 O2
Ligand molecular weight: 283.285
Ligand SMILES: CC1=C(C=NC2=CC(=O)NN12)C(=O)Nc3ccc(cc3)N
Ligand InChI: InChI=1S/C14H13N5O2/c1-8-11(7-16-12-6-13(20)18-19(8)12)14(21)17-10-4-2-9(15)3-5-10/h2-7H,15H2,1H3,(H,17,21)(H,18,20)
Release date: 2023-02-15