satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of MUS81-EME1 bound by compound 15. (PDB entry 9F9K)
Macromolecule: Crossover junction endonuclease MUS81
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.22
Sequence length: 308 residues
Sequence: GSSAELASEAGVQQQPLELRPGEYRVLLCVDIGETRGGGHRPELLRELQRLHVTHTVRKLHVGDFVWVAQETNPRDPANPGELVLDHIVERKRLDDLCSSIIDGRFREQKFRLKRCGLERRVYLVEEHGSVHNLSLPESTLLQAVTNTQVIDGFFVKRTADIKESAAYLALLTRGLQRLYQGHTLRSRPWGTPGNPESGAMTSPNPLCSLLTFSDFNAGAIKNKAQSVREVFARQLMQVRGVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTLSQLYCSYGPLT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.728
R work: 0.2327
R free: 0.2543
Average B factor: 70.97
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 12 % PEG8000, pH 5.5
Ligand: 5-oxidanyl-6-oxidanylidene-2-(4-phenylphenyl)-1H-pyrimidine-4-carboxylic acid (A1IA7)
Ligand formula: C17 H12 N2 O4
Ligand molecular weight: 308.288
Ligand SMILES: c1ccc(cc1)c2ccc(cc2)C3=NC(=C(C(=O)N3)O)C(=O)O
Ligand InChI: InChI=1S/C17H12N2O4/c20-14-13(17(22)23)18-15(19-16(14)21)12-8-6-11(7-9-12)10-4-2-1-3-5-10/h1-9,20H,(H,22,23)(H,18,19,21)
Release date: 2024-07-03
CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 1-[(3-chloro-4-fluorophenyl)carbonyl]-3,3-difluoro-5-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl}piperidine (PDB entry 5TZX)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 344 residues
Sequence: SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2475
R free: 0.3065
Average B factor: 22.632
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293
Crystal growth procedure: 17-19% PEG3350, 0.2M MgCl2, 0.1M Tris, pH 8.4
Matthews coefficient: 2.16
Solvent content (%): 43.11
Ligand: (3-chloro-4-fluorophenyl)[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl]methanone (7OY)
Ligand formula: C18 H15 Cl F3 N5 O
Ligand molecular weight: 409.793
Ligand SMILES: Cc1cc(n2c(n1)ncn2)C3CC(CN(C3)C(=O)c4ccc(c(c4)Cl)F)(F)F
Ligand InChI: InChI=1S/C18H15ClF3N5O/c1-10-4-15(27-17(25-10)23-9-24-27)12-6-18(21,22)8-26(7-12)16(28)11-2-3-14(20)13(19)5-11/h2-5,9,12H,6-8H2,1H3/t12-/m0/s1
Release date: 2017-02-22
Human PFKFB3 in complex with a N-Aryl 6-Aminoquinoxaline inhibitor 5 (PDB entry 6IBX)
Macromolecule: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.105
Sequence length: 429 residues
Sequence: ELTQSRVQKIWVPVNSPTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQYSSYNFFRPDNEEAMKVRKQCALAALRDVKSYLAKEGGQIAVFDATNTTRERRHMILHFAKENDFKAFFIESVCDDPTVVASNIMEVKISSPDYKDCNSAEAMDDFMKRISCYEASYQPLDPDKCDRDLSLIKVIDVGRRFLVNRVQDHIQSRIVYYLMNIHVQPRTIYLCRHGENEHNLQGRIGGDSGLSSRGKKFASALSKFVEEQNLKDLRVWTSQLKSTIQTAEALRLPYEQWKALNEIDAGVCEELTYEEIRDTYPEEYALREQDKYYYRYPTGESYQDLVQRLEPVIMELERQENVLVICHQAVLRCLLAYFLDKSAEEMPYLKCPLHTVLKLTPVAYGCRVESIYLNVESVCTHRERSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.1871
R free: 0.2199
Average B factor: 38.185
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 2% Tacsimate, 10% PEG3350, 0.1M MES/imidazole pH 7.0
Matthews coefficient: 3.89
Solvent content (%): 68.37
Ligand: 3-[[8-(1-methylindol-6-yl)quinoxalin-6-yl]amino]-~{N}-[(3~{S})-1-methylpiperidin-3-yl]pyridine-4-carboxamide (H9Z)
Ligand formula: C29 H29 N7 O
Ligand molecular weight: 491.587
Ligand SMILES: Cn1ccc2c1cc(cc2)c3cc(cc4c3nccn4)Nc5cnccc5C(=O)NC6CCCN(C6)C
Ligand InChI: InChI=1S/C29H29N7O/c1-35-12-3-4-21(18-35)34-29(37)23-7-9-30-17-26(23)33-22-15-24(28-25(16-22)31-10-11-32-28)20-6-5-19-8-13-36(2)27(19)14-20/h5-11,13-17,21,33H,3-4,12,18H2,1-2H3,(H,34,37)/t21-/m0/s1
Release date: 2019-01-23
Crystal structure of the methylated K125R/V301L AKR1B10 Holoenzyme (PDB entry 4XZN)
Macromolecule: Aldo-keto reductase family 1 member B10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 316 residues
Sequence: MATFVELSTKAKMPIVGLGTWKSPLGKVKEAVKVAIDAGYRHIDCAYVYQNEHEVGEAIQEKIQEKAVKREDLFIVSKLWPTFFERPLVRKAFEKTLKDLKLSYLDVYLIHWPQGFKSGDDLFPRDDKGNAIGGKATFLDAWEAMEELVDEGLVKALGVSNFSHFQIEKLLNKPGLKYKPVTNQVECHPYLTQEKLIQYCHSKGITVTAYSPLGSPDRPWAKPEDPSLLEDPKIKEIAAKHKKTAAQVLIRFHIQRNVIVIPKSVTPARIVENIQVFDFKLSDEEMATILSFNRNWRACNLLQSSHLEDYPFNAEY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1955
R free: 0.2283
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 100 mM sodium cacodylate
Matthews coefficient: 2.56
Solvent content (%): 52.04
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: 2015-11-18
Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor (PDB entry 5A09)
Macromolecule: NEUTROPHIL ELASTASE
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.37
Sequence length: 218 residues
Sequence: IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.18235
R free: 0.23944
Average B factor: 25.866
Crystal growth procedure: 28%PEG4000, 0.1MTRIS/HCL AT PH 8.2, 0.7MLICL
Matthews coefficient: 2.28
Solvent content (%): 46.1
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: 2015-08-19
STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM I IODIDE COMPLEX - 2.3A (PDB entry 4UYU)
Macromolecule: PROTEIN NOTUM HOMOLOG
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.1
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.20838
R free: 0.24346
Average B factor: 46.897
Crystallization pH: 7.5
Crystal growth procedure: 20 %W/V PEG 3350 0.1 M BT PROPANE PH 6.5 0.2 M NAI
Matthews coefficient: 2.31
Solvent content (%): 46.66
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: 2015-02-25
JAK2 JH2 in complex with a diaminopyrimidine (PDB entry 5UT6)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.645
R work: 0.1664
R free: 0.2059
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris, pH 8.0
0.2M Sodium acetate
12-20% PEG 4,000
Matthews coefficient: 2.2
Solvent content (%): 44.05
Ligand: 4-({4-amino-6-[3-(hydroxymethyl)-1H-pyrazol-1-yl]pyrimidin-2-yl}amino)benzonitrile (8MY)
Ligand formula: C15 H13 N7 O
Ligand molecular weight: 307.31
Ligand SMILES: c1cc(ccc1C#N)Nc2nc(cc(n2)n3ccc(n3)CO)N
Ligand InChI: InChI=1S/C15H13N7O/c16-8-10-1-3-11(4-2-10)18-15-19-13(17)7-14(20-15)22-6-5-12(9-23)21-22/h1-7,23H,9H2,(H3,17,18,19,20)
Release date: 2017-06-07
Crystal structure of the Pri1 subunit of human primase (PDB entry 6RB4)
Macromolecule: DNA primase small subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 410 residues
Sequence: GTSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1929
R free: 0.2148
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 100mM Bis Tris propane pH 6.5, 24 % PEG 3350, 150 mM NaF
Matthews coefficient: 2.35
Solvent content (%): 47.76
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: 2019-09-11
Crystal Structure of Factor VIIa in complex with 5-hydroxy-N-(3-oxo-1,2-dihydroisoindol-5-yl)-1-[3-[(phenylcarbamoylamino)methyl]phenyl]pyrazole-4-carboxamide (PDB entry 5PAN)
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): 1.62
R work: 0.1614
R free: 0.179
Average B factor: 23.252
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
Matthews coefficient: 3.77
Solvent content (%): 67.39
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
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 2-piperidin-4-yloxy-5-(trifluoromethyl)pyridine (N10072a) (ligand modelled based on PANDDA event map) (PDB entry 5FZA)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.099
R work: 0.1927
R free: 0.228
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.11
Solvent content (%): 41.72
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-03-30
JAK2 JH1 in complex with BL2-110 (PDB entry 6VSN)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1903
R free: 0.252
Average B factor: 40.8852
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350
Matthews coefficient: 3.03
Solvent content (%): 59.43
Ligand: (3S)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile (RG4)
Ligand formula: C17 H18 N6
Ligand molecular weight: 306.365
Ligand SMILES: c1c[nH]c2c1c(ncn2)c3cnn(c3)C(CC#N)C4CCCC4
Ligand InChI: InChI=1S/C17H18N6/c18-7-5-15(12-3-1-2-4-12)23-10-13(9-22-23)16-14-6-8-19-17(14)21-11-20-16/h6,8-12,15H,1-5H2,(H,19,20,21)/t15-/m0/s1
Release date: 2021-02-17
Structure of the unliganded form of the proprotein convertase furin in presence of EDTA. (PDB entry 5JXI)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 482 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1576
R free: 0.1851
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: crystallization solution: 100 mM MES, 200 mM K/NaH2PO4, pH 5.5-6.0, 3-4 M NaCl, 3% DMSO; reservoir solution: 3-4 M NaCl
Matthews coefficient: 3.76
Solvent content (%): 67.3
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: 2016-10-05
Crystal structure of human JARID1B in complex with S40650a (PDB entry 5LWB)
Macromolecule: Lysine-specific demethylase 5B,Lysine-specific demethylase 5B,Lysine-specific demethylase 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 481 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKINK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.1822
R free: 0.2177
Average B factor: 57.4458
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.8M Pottassium Phosphate- dibasic, 0.8M Sodium Phosphate monobasic
Matthews coefficient: 4.4
Solvent content (%): 72.03
Ligand: 5-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile (79H)
Ligand formula: C17 H21 N7 O
Ligand molecular weight: 339.395
Ligand SMILES: CC(C)C1C(=Nc2c(cnn2C1=O)C#N)c3cnn(c3)CCN(C)C
Ligand InChI: InChI=1S/C17H21N7O/c1-11(2)14-15(13-9-19-23(10-13)6-5-22(3)4)21-16-12(7-18)8-20-24(16)17(14)25/h8-11,14H,5-6H2,1-4H3/t14-/m1/s1
Release date: 2016-10-26
Crystal structure of human 5' exonuclease Apollo (PDB entry 5AHO)
Macromolecule: 5' EXONUCLEASE APOLLO
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 336 residues
Sequence: SMNGVLIPHTPIAVDFWSLRRAGTARLFFLSHMHSDHTVGLSSTWARPLYCSPITAHLLHRHLQVSKQWIQALEVGESHVLPLDEIGQETMTVTLLDANHCPGSVMFLFEGYFGTILYTGDFRYTPSMLKEPALTLGKQIHTLYLDNTNCNPALVLPSRQEAAHQIVQLIRKHPQHNIKIGLYSLGKESLLEQLALEFQTWVVLSPRRLELVQLLGLADVFTVEEKAGRIHAVDHMEICHSNMLRWNQTHPTIAILPTSRKIHSSHPDIHVIPYSDHSSYSELRAFVAALKPCQVVPIVSRRPCGGFQDSLSPRISVPLIPDSVQQYMSSFSRKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.16
R work: 0.2059
R free: 0.2257
Crystal growth procedure: 0.4M K/NA(TART)
Matthews coefficient: 3.22
Solvent content (%): 61.82
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: 2015-02-18
MTH1 in complex with TH012532 (PDB entry 8A0T)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.21164
R free: 0.25265
Average B factor: 30.239
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 30 % PEG6000, 0.1 M sodium acetate trihydrate pH 3.5, 0.2 M lithium sulphate
Matthews coefficient: 2.18
Solvent content (%): 43.45
Ligand: 5-(phenylmethyl)pyrimidine-2,4-diol (KLO)
Ligand formula: C11 H10 N2 O2
Ligand molecular weight: 202.209
Ligand SMILES: c1ccc(cc1)Cc2cnc(nc2O)O
Ligand InChI: InChI=1S/C11H10N2O2/c14-10-9(7-12-11(15)13-10)6-8-4-2-1-3-5-8/h1-5,7H,6H2,(H2,12,13,14,15)
Release date: 2023-09-13
Crystal structure of SETDB1 with a modified H3 peptide (PDB entry 6BHH)
Macromolecule: Histone-lysine N-methyltransferase SETDB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 239 residues
Sequence: MHHHHHHSSGRENLYFQGGELSKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEAEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMKTSSASALE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1925
R free: 0.2374
Average B factor: 23.469
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M HEPES
Matthews coefficient: 2.35
Solvent content (%): 47.64
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: 2017-11-22
Crystal Structure of the Mib Repeat Domain of Mind bomb 1 (PDB entry 4TSE)
Macromolecule: E3 ubiquitin-protein ligase MIB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 174 residues
Sequence: GPLGSRNPGGLQIGDLVNIDLDLEIVQSLQHGHGGWTDGMFETLTTTGTVCGIDEDHDIVVQYPSGNRWTFNPAVLTKANIVRSGDAAQGAEGGTSQFQVGDLVQVCYDLERIKLLQRGHGEWAEAMLPTLGKVGRVQQIYSDSDLKVEVCGTSWTYNPAAVSKVASAGSAISN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.057
R work: 0.1897
R free: 0.2293
Average B factor: 18.72
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 293
Crystal growth procedure: 24% v/v PEK2K MME, 0.8M HCOONa using 6 mg/ml protein
Matthews coefficient: 2.6
Solvent content (%): 52.6
Release date: 2015-03-18
Crystal structure of bruton agammaglobulinemia tyrosine kinase complexed with BMS-824171 AKA 6-[(3R)-3-(4-tert-bu tylbenzamido)piperidin-1-yl]-2-{[4-(morpholine-4-carbonyl) phenyl]amino}pyridine-3-carboxamide (PDB entry 5BPY)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 267 residues
Sequence: GHMEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.214
R free: 0.2423
Average B factor: 32.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 25% MEPEG5K, pH 8.0, 298K, Vapor Diffusion, Hanging Drop
Matthews coefficient: 2.3
Solvent content (%): 46.43
Ligand: 6-{(3R)-3-[(4-tert-butylbenzoyl)amino]piperidin-1-yl}-2-{[4-(morpholin-4-ylcarbonyl)phenyl]amino}pyridine-3-carboxamide (4UQ)
Ligand formula: C33 H40 N6 O4
Ligand molecular weight: 584.708
Ligand SMILES: CC(C)(C)c1ccc(cc1)C(=O)NC2CCCN(C2)c3ccc(c(n3)Nc4ccc(cc4)C(=O)N5CCOCC5)C(=O)N
Ligand InChI: InChI=1S/C33H40N6O4/c1-33(2,3)24-10-6-22(7-11-24)31(41)36-26-5-4-16-39(21-26)28-15-14-27(29(34)40)30(37-28)35-25-12-8-23(9-13-25)32(42)38-17-19-43-20-18-38/h6-15,26H,4-5,16-21H2,1-3H3,(H2,34,40)(H,35,37)(H,36,41)/t26-/m1/s1
Release date: 2015-09-23
Carbonic anhydrase inhibitors: Design and synthesis of new heteroaryl-N-carbonylbenzenesulfonamides targeting druggable human carbonic anhydrase isoforms (hCA VII, hCA IX, and hCA XIV) (PDB entry 4Z0Q)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1464
R free: 0.1914
Average B factor: 12.374
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 50mM Tris-HCl, 1,6 M Sodium Citrate
Matthews coefficient: 2.12
Solvent content (%): 42.09
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2015-08-26