satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human tankyrase 2 in complex with 5-amino-3- pentyl-1,2-dihydroisoquinolin-1-one (PDB entry 4UVS)
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): 2
R work: 0.18164
R free: 0.21424
Average B factor: 16.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
Matthews coefficient: 2.4
Solvent content (%): 49
Ligand: 5-amino-3-pentylisoquinolin-1(2H)-one (R4E)
Ligand formula: C14 H18 N2 O
Ligand molecular weight: 230.306
Ligand SMILES: CCCCCC1=Cc2c(cccc2N)C(=O)N1
Ligand InChI: InChI=1S/C14H18N2O/c1-2-3-4-6-10-9-12-11(14(17)16-10)7-5-8-13(12)15/h5,7-9H,2-4,6,15H2,1H3,(H,16,17)
Release date: 2015-07-29
Crystal structure of the p110alpha catalytic subunit from homo sapiens in complex with activator 1938 (PDB entry 8OW2)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.137
Sequence length: 946 residues
Sequence: GSVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKDTPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.57
R work: 0.2128
R free: 0.2714
Average B factor: 83.11
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 12.5% (w/v) PEG 4K, 20% (v/v) 1,2,6-hexanetriol, 50 mM Polyamines, 0.1 M MOPSO/bis-tris pH 6.5
Matthews coefficient: 2.61
Solvent content (%): 52.81
Ligand: 1-[7-[[2-[[4-(4-ethylpiperazin-1-yl)phenyl]amino]pyridin-4-yl]amino]-2,3-dihydroindol-1-yl]ethanone (QIH)
Ligand formula: C27 H32 N6 O
Ligand molecular weight: 456.583
Ligand SMILES: CCN1CCN(CC1)c2ccc(cc2)Nc3cc(ccn3)Nc4cccc5c4N(CC5)C(=O)C
Ligand InChI: InChI=1S/C27H32N6O/c1-3-31-15-17-32(18-16-31)24-9-7-22(8-10-24)30-26-19-23(11-13-28-26)29-25-6-4-5-21-12-14-33(20(2)34)27(21)25/h4-11,13,19H,3,12,14-18H2,1-2H3,(H2,28,29,30)
Release date: 2023-05-24
Abl kinase in complex with SKI and asciminib (PDB entry 8SSN)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 448 residues
Sequence: GNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNYDKWEMERTDITMKHKLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDYLRECNRQEVNAVVLLYMATQISSAMEYLEKKNFIHRDLAARNCLVGENHLVKVADFGLSRLMTGDTYTAHAGAKFPIKWTAPESLAYNKFSIKSDVWAFGVLLWEIATYGMSPYPGIDLSQVYELLEKDYRMERPEGCPEKVYELMRACWQWNPSDRPSFAEIHQAFETMFQESSISDEVEKEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.86
R work: 0.2977
R free: 0.348
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291.15
Crystal growth procedure: Crystals of AblFL in complex with SKI and asciminib were obtained by combining 0.3 ul of 600 uM AblFL + 700 uM SKI + 700 uM asciminib (~32 mg/ml) in 5 percent DMSO with 0.4 ul reservoir of 0.1 M Tris-HCl pH 8 + 1.75 M Ammonium sulfate + 2 percent (v/v) polypropylene glycol 400 (PPG 400). The final stock of complex was concentrated from 1 uM AblFL with ~1.2 uM SKI/asciminib after incubation at 4 degree C for 6 h. Screening around this condition yielded crystals in a transparent diamond-shaped or plate-shaped crystals. Crystals were grown at 18 degree C by sitting drop for a few days. The crystals were transferred to a drop of fresh reservoir containing 20 percent Xylitol with matching concentration of inhibitors in 5 percent DMSO for few seconds for cryo-protection
Matthews coefficient: 2.52
Solvent content (%): 51.21
Ligand: asciminib (AY7)
Ligand formula: C20 H18 Cl F2 N5 O3
Ligand molecular weight: 449.838
Ligand SMILES: c1cc(ccc1NC(=O)c2cc(c(nc2)N3CCC(C3)O)c4ccn[nH]4)OC(F)(F)Cl
Ligand InChI: InChI=1S/C20H18ClF2N5O3/c21-20(22,23)31-15-3-1-13(2-4-15)26-19(30)12-9-16(17-5-7-25-27-17)18(24-10-12)28-8-6-14(29)11-28/h1-5,7,9-10,14,29H,6,8,11H2,(H,25,27)(H,26,30)/t14-/m1/s1
Release date: 2023-09-06
Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP (PDB entry 6E3X)
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): 2.65
R work: 0.192
R free: 0.266
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 14% TO 23% PEG3400, AND 350 MM SODIUM
 ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING
 DROP, TEMPERATURE 298K
Matthews coefficient: 2.41
Solvent content (%): 48.98
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2019-04-03
Crystal structure of human JMJD2A in complex with compound 40 (PDB entry 5A80)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 381 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.1901
R free: 0.2489
Crystallization pH: 8.5
Crystal growth procedure: 30% PEG3350, 0.1M TRIS PH 8.5, 0.2M AMMONIUM SULFATE
Matthews coefficient: 2.69
Solvent content (%): 54.29
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2016-01-13
Structure of Get3 bound to the transmembrane domain of Pep12 (PDB entry 4XTR)
Macromolecule: ATPase GET3
Type: Protein, polypeptide(L)
Source organism: Saccharomyces cerevisiae S288C
EC number: 3.6
Sequence length: 354 residues
Sequence: MDLTVEPNLHSLITSTTHKWIFVGGKGGVGKTTSSCSIAIQMALSQPNKQFLLISTNPAHNLSDAFGEKFGKDARKVTGMNNLSCMEIDPSAALKDMNDMAVSRANNNGSDGQGDDLGSLLQGGALADLTGSIPGIDEALSFMEVMKHIKRQEQGEGETFDTVIFDTAPTGHTLRFLQLPNTLSKLLEKFGEITNKLGPMLNSFMGAGNVDISGKLNELKANVETIRQQFTDPDLTTFVCVCISEFLSLYETERLIQELISYDMDVNSIIVNQLLFAENDQEHNCKRCQARWKMQKKYLDQIDELYEDFHVVKMPLCAGEIRGLNNLTKFSQFLNKEYNPITDGKVIYELEDKE
Oligomeric state: Hetero 7-mer
Stoichiometry: A2, B2, C2, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1872
R free: 0.2161
Average B factor: 56.7877
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 2 mM ATP and 2 mM MgCl2 with 15% PEG 3350, 25 mM succinic acid pH 7.0
Matthews coefficient: 2.67
Solvent content (%): 53.9
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2015-03-18
Crystal Structure of human phosphodiesterase 10 in complex with N-(6-methylpyridin-2-yl)-5-pyridin-3-yl-1,7-naphthyridin-8-amine (PDB entry 5SHK)
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): 2
R work: 0.1887
R free: 0.2181
Average B factor: 39.954
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: 2.61
Solvent content (%): 52.8
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
Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor. (PDB entry 5OHJ)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 421 residues
Sequence: MSVSEMASNKFKRMLNRELTHLSEMSRSGNQVSEYISNTFLDKQNDVEIPKVTAEEAPQPMTQISGVKKLMHSSSLNNTSISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1841
R free: 0.21153
Average B factor: 22.688
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: Drops comprised 2microliters protein solution mixed with reservoir buffer consisting of 100mM sodium acetate pH 4.5, 14% PEG400 and 50mM calcium acetate. After 2 days they were streak seeded with crystals obtained from rolipram complex seed stock. Crystals, up to 100 microns in largest dimension, grew from precipitate after 1-2 weeks. Crystals were transferred to a cryoprotectant solution (100mM sodium acetate pH 4.5, 14% PEG400, 50mM calcium acetate and 20% glycerol) then flash-frozen prior to X-ray data collection.
Matthews coefficient: 1.8
Solvent content (%): 31.5
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: 2017-12-13
ITK kinase domain in complex with compound 1 N-{1-[(1,1-dioxo-1-thian-2-yl)(phenyl)methyl]-1H- pyrazol-4-yl}-5,5-difluoro-5a-methyl-1H,4H,4aH,5H,5aH,6H-cyclopropa[f]indazole-3-carboxamide (PDB entry 4RFM)
Macromolecule: Tyrosine-protein kinase ITK/TSK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 266 residues
Sequence: GSVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFEFMEHGCLSDYLRTQRGLFAAETLLGMCLDVCEGMAYLEEASVIHRDLAARNCLVGENQVIKVSDFGMTRFVLDDQYTSSTGTKFPVKWASPEVFSFSRYSSKSDVWSFGVLMWEVFSEGKIPYENRSNSEVVEDISTGFRLYKPRLASTHVYQIMNHCWKERPEDRPAFSRLLRQLAAIAASGL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.20265
R free: 0.26362
Average B factor: 37.73
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Magnesium Chloride, 0.1 M Tris.HCl (pH 8.0), 20 % PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Matthews coefficient: 2.01
Solvent content (%): 38.74
Ligand: (4aS,5aR)-N-{1-[(R)-[(2R)-1,1-dioxidotetrahydro-2H-thiopyran-2-yl](phenyl)methyl]-1H-pyrazol-4-yl}-5,5-difluoro-5a-methyl-1,4,4a,5,5a,6-hexahydrocyclopropa[f]indazole-3-carboxamide (3P6)
Ligand formula: C25 H27 F2 N5 O3 S
Ligand molecular weight: 515.575
Ligand SMILES: CC12Cc3c(c(n[nH]3)C(=O)Nc4cnn(c4)C(c5ccccc5)C6CCCCS6(=O)=O)CC1C2(F)F
Ligand InChI: InChI=1S/C25H27F2N5O3S/c1-24-12-18-17(11-20(24)25(24,26)27)21(31-30-18)23(33)29-16-13-28-32(14-16)22(15-7-3-2-4-8-15)19-9-5-6-10-36(19,34)35/h2-4,7-8,13-14,19-20,22H,5-6,9-12H2,1H3,(H,29,33)(H,30,31)/t19-,20+,22-,24-/m1/s1
Release date: 2015-04-29
Human Carbonic Anhydrase I in complex with 4-(5-acetyl-6-methyl-2-oxo-1,2,3,4-tetrahydropyrimidin-4-yl)benzenesulfonamide (PDB entry 8QGV)
Macromolecule: Carbonic anhydrase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 261 residues
Sequence: MASPDWGYDDKNGPEQWSKLYPIANGNNQSPVDIKTSETKHDTSLKPISVSYNPATAKEIINVGHSFHVNFEDNDNRSVLKGGPFSDSYRLFQFHFHWGSTNEHGSEHTVDGVKYSAELHVAHWNSAKYSSLAEAASKADGLAVIGVLMKVGEANPKLQKVLDALQAIKTKGKRAPFTNFDPSTLLPSSLDFWTYPGSLTHPPLYESVTWIICKESISVSSEQLAQFRSLLSNVEGDNAVPMQHNNRPTQPLKGRTVRASF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1978
R free: 0.2403
Average B factor: 31.709
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 296
Crystal growth procedure: 28-31% PEG4000, 0.2 M sodium acetate, 0.1 M Tris pH 8.5-9.0
Matthews coefficient: 2.34
Solvent content (%): 47.47
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: 2024-09-11
C57D/C146D mutant of Human Cu, Zn Superoxide Dismutase (SOD1) (PDB entry 7FB6)
Macromolecule: Superoxide dismutase [Cu-Zn]
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.15.1.1
Sequence length: 161 residues
Sequence: GAMDPEFMATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGDTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLADGVIGIAQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1843
R free: 0.213
Average B factor: 20.86
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 287.15
Crystal growth procedure: 0.2M MgCl2, 22% (w/v) PEG 3350
Matthews coefficient: 1.96
Solvent content (%): 37.36
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
human factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-1-[3-[[(3,5-dimethyl-1,2-oxazol-4-yl)carbamoylamino]methyl]phenyl]-5-hydroxypyrazole-4-carboxamide at 1.73A (PDB entry 5PAI)
Macromolecule: Coagulation factor VII light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 64 residues
Sequence: LICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKRNASKPQGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.1638
R free: 0.1815
Average B factor: 19.972
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
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: 2017-06-21
Human steroidogenic cytochrome P450 17A1 with 3-keto-5alpha-abiraterone analog (PDB entry 6WW0)
Macromolecule: Steroid 17-alpha-hydroxylase/17,20 lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.19
Sequence length: 494 residues
Sequence: MAKKTGAKYPKSLLSLPLVGSLPFLPRHGHMHNNFFKLQKKYGPIYSVRMGTKTTVIVGHHQLAKEVLIKKGKDFSGRPQMATLDIASNNRKGIAFADSGAHWQLHRRLAMATFALFKDGDQKLEKIICQEISTLCDMLATHNGQSIDISFPVFVAVTNVISLICFNTSYKNGDPELNVIQNYNEGIIDNLSKDSLVDLVPWLKIFPNKTLEKLKSHVKIRNDLLNKILENYKEKFRSDSITNMLDTLMQAKMNSDNGNAGPDQDSELLSDNHILTTIGDIFGAGVETTTSVVKWTLAFLLHNPQVKKKLYEEIDQNVGFSRTPTISDRNRLLLLEATIREVLRLRPVAPMLIPHKANVDSSIGEFAVDKGTEVIINLWALHHNEKEWHQPDQFMPERFLNPAGTQLISPSVSYLPFGAGPRSCIGEILARQELFLIMAWLLQRFDLEVPDDGQLPSLEGIPKVVFLIDSFKVKIKVRQAWREAQAEGSTHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.1854
R free: 0.2184
Average B factor: 34.58
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 175 mM Tris HCl (pH = 8.5), 30% PEG 3350, 300 mM LiSO4, 3% glycerol
Matthews coefficient: 2.6
Solvent content (%): 52.74
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2021-05-26
Crystal Structure of Factor VIIa in complex with 2-phenyl-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-3-ol (PDB entry 5PB2)
Macromolecule: Coagulation factor VII light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 64 residues
Sequence: LICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKRNASKPQGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1958
R free: 0.2036
Average B factor: 17.747
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
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: 2017-06-21
CDK2 in complex with Cpd14 (5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)-N-(5-(4-methylpiperazin-1-yl)pyridin-2-yl)pyrimidin-2-amine) (PDB entry 6OQI)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 299 residues
Sequence: FMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1975
R free: 0.2411
Average B factor: 53.7083
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 10-12% PEG 4K, 50 mM Hepes pH7.5, 50 mM Ammonia Acetate
Matthews coefficient: 2.03
Solvent content (%): 39.45
Ligand: 5-fluoro-N-[5-(4-methylpiperazin-1-yl)pyridin-2-yl]-4-[(4S)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine (N14)
Ligand formula: C23 H29 F N8
Ligand molecular weight: 436.528
Ligand SMILES: CC1CCCCn2c1c(cn2)c3c(cnc(n3)Nc4ccc(cn4)N5CCN(CC5)C)F
Ligand InChI: InChI=1S/C23H29FN8/c1-16-5-3-4-8-32-22(16)18(14-27-32)21-19(24)15-26-23(29-21)28-20-7-6-17(13-25-20)31-11-9-30(2)10-12-31/h6-7,13-16H,3-5,8-12H2,1-2H3,(H,25,26,28,29)/t16-/m0/s1
Release date: 2020-07-29
Human p38alpha MAP Kinase in Complex with Dibenzosuberone Compound 2 (PDB entry 5TBE)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.44
R work: 0.18634
R free: 0.25381
Average B factor: 37.457
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, 21-29 % PEG4000, 25 mM BOG
Matthews coefficient: 1.95
Solvent content (%): 36.93
Ligand: ~{N}-[2,4-bis(fluoranyl)-5-[[9-(2-morpholin-4-ylethylcarbamoyl)-11-oxidanylidene-5,6-dihydrodibenzo[1,2-~{d}:1',2'-~{f}][7]annulen-3-yl]amino]phenyl]thiophene-2-carboxamide (78L)
Ligand formula: C33 H30 F2 N4 O4 S
Ligand molecular weight: 616.678
Ligand SMILES: c1cc(sc1)C(=O)Nc2cc(c(cc2F)F)Nc3ccc4c(c3)CCc5ccc(cc5C4=O)C(=O)NCCN6CCOCC6
Ligand InChI: InChI=1S/C33H30F2N4O4S/c34-26-18-27(35)29(38-33(42)30-2-1-15-44-30)19-28(26)37-23-7-8-24-21(16-23)5-3-20-4-6-22(17-25(20)31(24)40)32(41)36-9-10-39-11-13-43-14-12-39/h1-2,4,6-8,15-19,37H,3,5,9-14H2,(H,36,41)(H,38,42)
Release date: 2017-04-19