satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of TNKS2 in complex with 7-chloro-2-{4-[(2-hydroxyethyl)(methyl)amino]phenyl}-3,4-dihydroquinazolin-4-one (PDB entry 5NWG)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 49 residues
Sequence: KMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.14134
R free: 0.16905
Average B factor: 20.718
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M LISO4, 0.1 M TRIS HCL, 24/26 %         PEG3350
Matthews coefficient: 2.45
Solvent content (%): 49.81
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: 2018-03-14
PCSK9(deltaCRD) in complex with cyclic peptide 51 (PDB entry 6XID)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 122 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.482
R work: 0.1868
R free: 0.2049
Average B factor: 22.13
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 200mM CaCl2, 100mM MES pH 6
Matthews coefficient: 2.58
Solvent content (%): 52.34
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2020-11-18
Crystal structure of PPM1K-N94K (PDB entry 6AK7)
Macromolecule: Protein phosphatase 1K, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 257 residues
Sequence: ISLAKVGCASQIGKRKENEDRFDFAQLTDEVLYFAVYDGHGGPAAADFCHTHMEKCIMDLLPKEANLETLLTLAFLEIDKAFSSHARLSADATLLTSGTTATVALLRDGIELVVASVGDSRAILCRKGKPMKLTIDHTPERADEKERIKKCGGFVAWNQPHVNGRLAMTRSIGDLDLKTSGVIAEPETKRIKLHHADDSFLVLTTDGINFMVNSQEICDFVNQCHDPNEAAHAVTEQAIQYGTEDNSTAVVVPFGAW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.605
R work: 0.1924
R free: 0.2243
Average B factor: 47.1155
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris, pH 8.5, 12% PEG 3350, 0.2 M MgCl2, 10 mM Mercaptoethanol
Matthews coefficient: 4.77
Solvent content (%): 74.19
Ligand: BETA-MERCAPTOETHANOL (BME)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: C(CS)O
Ligand InChI: InChI=1S/C2H6OS/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-09-11
Crystal Structure of human phosphodiesterase 10 in complex with N-(2-acetamido-1,3-benzothiazol-5-yl)-4-(azetidine-1-carbonyl)-2-methylpyrazole-3-carboxamide (PDB entry 5SFX)
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): 2.04
R work: 0.1765
R free: 0.2225
Average B factor: 39.958
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: 2.66
Solvent content (%): 53.72
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: 2022-10-12
Dibenzosuberone inhibitor 8e in complex with p38 MAPK (PDB entry 5MTY)
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): 2.31
R work: 0.21895
R free: 0.27131
Average B factor: 40.616
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM MES pH 5.6-6.3
20-30 % PEG4000
25 mM BOG
Matthews coefficient: 2.13
Solvent content (%): 42.31
Ligand: ~{N}-[2,4-bis(fluoranyl)-5-[[14-(2-hydroxyethylcarbamoyl)-2-oxidanylidene-6-tricyclo[9.4.0.0^{3,8}]pentadeca-1(15),3(8),4,6,11,13-hexaenyl]amino]phenyl]thiophene-2-carboxamide (HB9)
Ligand formula: C29 H23 F2 N3 O4 S
Ligand molecular weight: 547.572
Ligand SMILES: c1cc(sc1)C(=O)Nc2cc(c(cc2F)F)Nc3ccc4c(c3)CCc5ccc(cc5C4=O)C(=O)NCCO
Ligand InChI: InChI=1S/C29H23F2N3O4S/c30-22-14-23(31)25(34-29(38)26-2-1-11-39-26)15-24(22)33-19-7-8-20-17(12-19)5-3-16-4-6-18(13-21(16)27(20)36)28(37)32-9-10-35/h1-2,4,6-8,11-15,33,35H,3,5,9-10H2,(H,32,37)(H,34,38)
Release date: 2017-09-06
Crystal Structure of ERK2 in complex with 2-(1H-pyrazol-4-yl)-7-(pyridin-3-yl)-5H-pyrrolo[2,3-b]pyrazine (PDB entry 4QP8)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 369 residues
Sequence: MGSHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.446
R work: 0.204
R free: 0.2488
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG3350, 0.2 M proline, and 0.1 M HEPES pH7.5, in a 24-well Linbro plates incubated at 4C, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2
Solvent content (%): 38.54
Ligand: 2-(1H-pyrazol-4-yl)-7-(pyridin-3-yl)-5H-pyrrolo[2,3-b]pyrazine (362)
Ligand formula: C14 H10 N6
Ligand molecular weight: 262.269
Ligand SMILES: c1cc(cnc1)c2c[nH]c3c2nc(cn3)c4c[nH]nc4
Ligand InChI: InChI=1S/C14H10N6/c1-2-9(4-15-3-1)11-7-16-14-13(11)20-12(8-17-14)10-5-18-19-6-10/h1-8H,(H,16,17)(H,18,19)
Release date: 2015-09-23
EGFR-KINASE IN COMPLEX WITH COMPOUND 5 (PDB entry 6S9C)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: SMGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.73
R work: 0.2002
R free: 0.2248
Average B factor: 64.013
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 10 % PEG 10000
8 % ethylene glycol
0.1 M HEPES
Matthews coefficient: 3.5
Solvent content (%): 64.84
Ligand: ~{N}-[1-(2-methyl-2-oxidanyl-propyl)benzimidazol-2-yl]-2-phenyl-pyridine-4-carboxamide (L1K)
Ligand formula: C23 H22 N4 O2
Ligand molecular weight: 386.446
Ligand SMILES: CC(C)(Cn1c2ccccc2nc1NC(=O)c3ccnc(c3)c4ccccc4)O
Ligand InChI: InChI=1S/C23H22N4O2/c1-23(2,29)15-27-20-11-7-6-10-18(20)25-22(27)26-21(28)17-12-13-24-19(14-17)16-8-4-3-5-9-16/h3-14,29H,15H2,1-2H3,(H,25,26,28)
Release date: 2019-11-20
Human Argonaute-2 Bound to a Modified siRNA (PDB entry 5JS2)
Macromolecule: Protein argonaute-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26
Sequence length: 859 residues
Sequence: MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.954
R work: 0.2223
R free: 0.2611
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG 3350, 75mM Phenol, 12% Isopropanol, 100mM Tris
Matthews coefficient: 2.29
Solvent content (%): 46.31
Ligand: PHENOL (IPH)
Ligand formula: C6 H6 O
Ligand molecular weight: 94.111
Ligand SMILES: c1ccc(cc1)O
Ligand InChI: InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
Release date: 2016-07-20
Structure of Human Adenosine Deaminase Acting on dsRNA (ADAR2) bound to dsRNA containing a 2'-deoxy Benner's Base Z opposite the edited base (PDB entry 7KFN)
Macromolecule: Double-stranded RNA-specific editase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.4.37
Sequence length: 403 residues
Sequence: LHLDQTPSRQPIPSEGLQLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGEGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLTP
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1707
R free: 0.2256
Average B factor: 46.536
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM MES:NaOH pH 6.5, 18% PEG 20,000
Matthews coefficient: 2.76
Solvent content (%): 54.98
Ligand: INOSITOL HEXAKISPHOSPHATE (IHP)
Ligand formula: C6 H18 O24 P6
Ligand molecular weight: 660.035
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C6H18O24P6/c7-31(8,9)25-1-2(26-32(10,11)12)4(28-34(16,17)18)6(30-36(22,23)24)5(29-35(19,20)21)3(1)27-33(13,14)15/h1-6H,(H2,7,8,9)(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)(H2,19,20,21)(H2,22,23,24)/t1-,2-,3-,4+,5-,6-
Release date: 2021-06-16
delta-N METTL16 MTase domain (PDB entry 6GFK)
Macromolecule: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.346
Sequence length: 251 residues
Sequence: RVSLNFKDPEAVRALTCTLLREDFGLSIDIPLERLIPTVPLRLNYIHWVEDLIGHQDSDKSTLRRGIDIGTGASCIYPLLGATLNGWYFLATEVDDMCFNYAKKNVEQNNLSDLIKVVKVPQKTLLMDALKEESEIIYDFCMCNPPFFANQLEAKGVNSRNPRRPPPSSVNTGGITEIMAEGGELEFVKRIIHDSLQLKKRLRWYSCMLGKKCSLAPLKEELRIQGVPKVTYTEFCQGRTMRWALAWSFYD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.195
R free: 0.228
Average B factor: 67.16
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 1.7M Ammonium Sulfate, 0.2M K/Na Tartrate, 0.1M Na Citrate
Matthews coefficient: 2.35
Solvent content (%): 47.6
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2018-09-19
PIM1 in complex with Cpd36 ((1S,3S)-N1-(6-(5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl)pyridin-2-yl)cyclohexane-1,3-diamine) (PDB entry 5DIA)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 299 residues
Sequence: MKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSKKLAAALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.964
R work: 0.196
R free: 0.2286
Average B factor: 41.1516
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 289
Crystal growth procedure: PEG 4000, 0.2M LiSO4, 0.1M Tris-HCl
Matthews coefficient: 3.19
Solvent content (%): 61.4
Ligand: (1S,3S)-N-{6-[5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl]pyridin-2-yl}cyclohexane-1,3-diamine (5E6)
Ligand formula: C22 H23 N7
Ligand molecular weight: 385.465
Ligand SMILES: c1cc(nc(c1)NC2CCCC(C2)N)c3c4cc(ncc4[nH]n3)c5cccnc5
Ligand InChI: InChI=1S/C22H23N7/c23-15-5-1-6-16(10-15)26-21-8-2-7-18(27-21)22-17-11-19(14-4-3-9-24-12-14)25-13-20(17)28-29-22/h2-4,7-9,11-13,15-16H,1,5-6,10,23H2,(H,26,27)(H,28,29)/t15-,16-/m0/s1
Release date: 2015-10-28
Crystal Structure of human phosphodiesterase 10 in complex with 2-chloro-6-(cyclopropylamino)-N-(2-phenyl-[1,2,4]triazolo[1,5-a]pyridin-7-yl)pyridine-4-carboxamide (PDB entry 5SKG)
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): 2.03
R work: 0.1835
R free: 0.2218
Average B factor: 38.753
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: 2.62
Solvent content (%): 53.12
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
crystal structure of human carbonic anhydrase I in complex with 4-(3-(2-((2-fluorobenzyl)amino)ethyl)ureido) benzenesulfonamide (PDB entry 6Y00)
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): 1.37
R work: 0.1978
R free: 0.2184
Average B factor: 25.33
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 200 mM Na-acetate, 30% PEG 4000, 100 mM Tris-HCl pH 9.
Inhibitor: 150 mM NaCl, 10% DMSO,  50 mM Tris pH 7
Matthews coefficient: 2.34
Solvent content (%): 47.46
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-09-23
Co-crystal structure of SHP2 in complex with a Cefsulodin derivative (PDB entry 4RDD)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 275 residues
Sequence: LYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.601
R work: 0.1751
R free: 0.2011
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 33 mM citric acid, 67 mM BIS-TRIS propane, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 2.2
Solvent content (%): 44.13
Ligand: 1-({(2R)-4-carboxy-2-[(R)-carboxy{[(2R)-2-phenyl-2-sulfoacetyl]amino}methyl]-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyr
idinium (3LU)
Ligand formula: C21 H22 N3 O8 S2
Ligand molecular weight: 508.545
Ligand SMILES: c1ccc(cc1)C(C(=O)NC(C2NC(=C(CS2)C[n+]3ccccc3)C(=O)O)C(=O)O)S(=O)(=O)O
Ligand InChI: InChI=1S/C21H21N3O8S2/c25-18(17(34(30,31)32)13-7-3-1-4-8-13)22-16(21(28)29)19-23-15(20(26)27)14(12-33-19)11-24-9-5-2-6-10-24/h1-10,16-17,19,23H,11-12H2,(H3-,22,25,26,27,28,29,30,31,32)/p+1/t16-,17+,19+/m0/s1
Release date: 2015-07-01
GDP-bound KRAS G12D in complex with TH-Z835 (PDB entry 7EWB)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: GMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1949
R free: 0.246
Average B factor: 31.239
Crystallization method: EVAPORATION
Crystallization temperature (K): 297
Crystal growth procedure: 0.2 M sodium acetate, 0.1 M Tris, pH 8.5, 26 % (w/v) PEG 3350
Matthews coefficient: 2.2
Solvent content (%): 44.17
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: 2021-12-29
Crystal structure of hDM2 in complex with a C-terminal triurea capped peptide chimera foldamer. (PDB entry 6HFA)
Macromolecule: LM266, 1-[(2~{S})-2-azanyl-3-methyl-butyl]urea
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 11 residues
Sequence: TSFAEYWXXXX
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1908
R free: 0.2384
Average B factor: 37.7329
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 90 mM HEPES, 1.26 M Na Citrate, 10% glycerol. Cryo: +30% Glycerol
Matthews coefficient: 1.8
Solvent content (%): 31.82
Release date: 2020-07-08
Crystal Structure of wild-type KRAS (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (crystal form II) (PDB entry 6XHB)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 170 residues
Sequence: GMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1863
R free: 0.2213
Average B factor: 62.1845
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM sodium cacodylate pH 6.5, 200 mM sodium citrate, 15% 2-propanol, 0.25% (w/v) n-octyl-beta-D-glucoside, 0.35 mM D-myo-phosphatidylinositol 3,4,5-triphosphate, and 0.25% (w/v) n-dodecyl-beta-D-maltoside
Matthews coefficient: 3.27
Solvent content (%): 62.44
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2021-01-13
X-RAY STRUCTURE OF SMYD3 in complex with benzodiazepine-type inhibitor 6 (PDB entry 7O2B)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.354
Sequence length: 428 residues
Sequence: MEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.204
R free: 0.258
Average B factor: 29.1249
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 8 % PEG 3350, 50 mM magnesium formate, 100 mM Tris pH 7.5
Matthews coefficient: 2.24
Solvent content (%): 45.14
Ligand: (2S)-N-butyl-1-(2-fluorophenyl)carbonyl-2-methyl-4-oxidanylidene-3,5-dihydro-2H-1,5-benzodiazepine-7-carboxamide (UZQ)
Ligand formula: C22 H24 F N3 O3
Ligand molecular weight: 397.443
Ligand SMILES: CCCCNC(=O)c1ccc2c(c1)NC(=O)CC(N2C(=O)c3ccccc3F)C
Ligand InChI: InChI=1S/C22H24FN3O3/c1-3-4-11-24-21(28)15-9-10-19-18(13-15)25-20(27)12-14(2)26(19)22(29)16-7-5-6-8-17(16)23/h5-10,13-14H,3-4,11-12H2,1-2H3,(H,24,28)(H,25,27)/t14-/m0/s1
Release date: 2021-07-07