satarupa22/MacromolecularLigandDB huggingface dataset:
The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me0 peptide (PDB entry 7W67)
Macromolecule: Set1/Ash2 histone methyltransferase complex subunit ASH2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 184 residues
Sequence: SRVLLALHDRAPQLKISDDRLTVVGEKGYSMVRASHGVRKGAWYFEITVDEMPPDTAARLGWSQPLGNLQAPLGYDKFSYSWRSKKGTKFHQSIGKHYSSGYGQGDVLGFYINLPEDTISGRGSSEIIFYKNGVNQGVAYKDIFEGVYFPAISLYKSCTVSINFGPCFKYPPKDLTYRPMSDMG
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.194
R work: 0.175
R free: 0.2219
Average B factor: 48.0675
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M Sodium chloride, 0.1 M HEPES, pH 7.5, 25% w/v polyethylene glycol 3350
Matthews coefficient: 2.05
Solvent content (%): 45.51
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: 2022-09-07
Identification of a New Zinc Binding Chemotype by Fragment Screening (PDB entry 5TY9)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.12964
R free: 0.18145
Average B factor: 14.416
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 281
Crystal growth procedure: the reservoir condition consisted of 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3; concentrated CA II at ~10 mg mL-1 was set up with seeding; dry compound was added to crystals several days before harvesting and data collection
Matthews coefficient: 2.11
Solvent content (%): 41.57
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2017-08-30
Structure of Apo Human SIRT5 (PDB entry 8GBL)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 271 residues
Sequence: KMARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.215
R free: 0.256
Average B factor: 37.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES 6.5, 25% PEG 4K
Matthews coefficient: 2.22
Solvent content (%): 44.67
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: 2024-06-05
Carbonic Anhydrase II complexed with 4-(2-(3-(4-fluorophenyl)ureido)ethylsulfonamido)benzenesulfonamide (PDB entry 7K6L)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.655
R work: 0.1743
R free: 0.2079
Average B factor: 18.3506
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 295
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris, pH 6.4
Matthews coefficient: 2.12
Solvent content (%): 42
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: 2020-12-23
Human Argonaute2 Bound to t1-Inosine Target RNA (PDB entry 4Z4G)
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): 2.7
R work: 0.1786
R free: 0.2244
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, Tris, Isopropanol, Phenol, Magnesium
Matthews coefficient: 2.13
Solvent content (%): 42.2
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: 2015-09-23
RING-DTC domains of Deltex 2, bound to ADP-ribose (PDB entry 6Y3J)
Macromolecule: Probable E3 ubiquitin-protein ligase DTX2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 235 residues
Sequence: GSEPEPEQVIKNYTEELKVPPDEDCIICMEKLSTASGYSDVTDSKAIGSLAVGHLTKCSHAFHLLCLLAMYCNGNKDGSLQCPSCKTIYGEKTGTQPQGKMEVLRFQMSLPGHEDCGTILIVYSIPHGIQGPEHPNPGKPFTARGFPRQCYLPDNAQGRKVLELLKVAWKRRLIFTVGTSSTTGETDTVVWNEIHHKTEMDRNITGHGYPDPNYLQNVLAELAAQGVTEDCLEQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2376
R free: 0.2822
Average B factor: 58.0141
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 292
Crystal growth procedure: Morpheus condition 39 (Molecular Dimensions)
Matthews coefficient: 2.32
Solvent content (%): 73.11
Ligand: ADENOSINE-5-DIPHOSPHORIBOSE (APR)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
Release date: 2020-09-02
Crystal structure of the PDE4D2 catalytic domain in complex with inhibitor (R)-Zl-n-91 (PDB entry 5WH5)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 327 residues
Sequence: TEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1931
R free: 0.2141
Average B factor: 26.926
Crystallization method: EVAPORATION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: The ~10mg/ml PDE4D2 (86-413) was stored in a buffer of 20 mM Tris.base, pH 7.5, 50 mM NaCl, 1 mM 2-mercaptoethanol, 1 mM EDTA and mixed with 2 mM (R)- or (S)-5. They were crystallized at 4C by hanging drop against a well buffer of 0.1 M HEPES pH 7.5, 15% PEG3350, 30% ethylene glycol, and 10% isopropanol.
Matthews coefficient: 2.58
Solvent content (%): 52.39
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: 2018-07-18
Crystal structure of LSD1-CoREST in complex with PRSFLVRR peptide (PDB entry 7CDD)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.76
R work: 0.20449
R free: 0.22733
Average B factor: 84.366
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
Release date: 2021-06-23
Human GAR transformylase in complex with GAR substrate and AGF362 inhibitor (PDB entry 8FJV)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.4.13
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.1917
R free: 0.2446
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris (pH 7.5), 0.333 mM NaCl, 20% polyethylene glycol (PEG) 4000, and 2% PEG 400
Matthews coefficient: 3.59
Solvent content (%): 65.74
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2023-09-06
Human PPARgamma ligand binding dmain complexed with SB1404 in a covalent bonded form (PDB entry 5DV6)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 287 residues
Sequence: GSHMAEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.20801
R free: 0.24409
Average B factor: 82.811
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 297
Crystal growth procedure: 2.2M sodium malonate pH 7.0
Matthews coefficient: 2.69
Solvent content (%): 54.24
Ligand: N-methylidene-3-nitrobenzamide (B4H)
Ligand formula: C8 H6 N2 O3
Ligand molecular weight: 178.145
Ligand SMILES: C=NC(=O)c1cccc(c1)[N+](=O)[O-]
Ligand InChI: InChI=1S/C8H6N2O3/c1-9-8(11)6-3-2-4-7(5-6)10(12)13/h2-5H,1H2
Release date: 2016-09-21
GTPase HRAS under 200 MPa pressure (PDB entry 7OGA)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.171
R free: 0.235
Average B factor: 36.34
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 40 mM Tris HCL, 10 mM MgCl2, 2 mM DTE, 26-30 % PEG-400
Matthews coefficient: 1.92
Solvent content (%): 35.83
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: 2022-02-09
Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors (PDB entry 5OW8)
Macromolecule: Group 10 secretory phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 123 residues
Sequence: GILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2157
R free: 0.2523
Average B factor: 23.132
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 37-45% PEG400
0.1M bis-Tris pH 5.6-5.9
Matthews coefficient: 2.23
Solvent content (%): 44.75
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: 2018-08-01
IRAK4 IN COMPLEX WITH inhibitor (PDB entry 6RFJ)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 322 residues
Sequence: MHHHHHHHENLYFQGENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.61
R work: 0.245
R free: 0.254
Average B factor: 92.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: pH7.5
Matthews coefficient: 2.56
Solvent content (%): 51.94
Ligand: methyl 4-[4-[[6-(cyanomethyl)-2-[(1-methylpyrazol-4-yl)amino]pyrido[3,2-d]pyrimidin-4-yl]amino]cyclohexyl]piperazine-1-carboxylate (K1E)
Ligand formula: C25 H32 N10 O2
Ligand molecular weight: 504.587
Ligand SMILES: Cn1cc(cn1)Nc2nc3ccc(nc3c(n2)NC4CCC(CC4)N5CCN(CC5)C(=O)OC)CC#N
Ligand InChI: InChI=1S/C25H32N10O2/c1-33-16-19(15-27-33)30-24-31-21-8-5-18(9-10-26)28-22(21)23(32-24)29-17-3-6-20(7-4-17)34-11-13-35(14-12-34)25(36)37-2/h5,8,15-17,20H,3-4,6-7,9,11-14H2,1-2H3,(H2,29,30,31,32)/t17-,20-
Release date: 2019-10-30
Carbonic Anhydrase II Inhibitor RA9 (PDB entry 5NXW)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1267
R free: 0.1554
Average B factor: 12.359
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris                                               
1.6 M Natrium Citrate
Matthews coefficient: 2.11
Solvent content (%): 41.65
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: 2018-01-17
Crystal Structure of Plk4 Kinase Domain Bound to Centrinone (PDB entry 4YUR)
Macromolecule: Serine/threonine-protein kinase PLK4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 278 residues
Sequence: GPGSATCIGEKIEDFKVGNLLGKGSFAGVYRAESIHTGLEVAIKMIDKKAMYKAGMVQRVQNEVKIHCQLKHPSILELYNYFEDSNYVYLVLEMCHNGEMNRYLKNRVKPFSENEARHFMHQIITGMLYLHSHGILHRDLTLSNLLLTRNMNIKIADFGLATQLKMPHEKHYTLCGTPNYISPEIATRSAHGLESDVWSLGCMFYTLLIGRPPFDTDTVKNTLNKVVLADYEMPSFLSIEAKDLIHQLLRRNPADRLSLSSVLDHPFMSRNSSTKSKD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1992
R free: 0.2695
Average B factor: 47.07
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 297
Crystal growth procedure: 0.1 M HEPES, 0.2 M MgCl2, 30% PEG 400
Matthews coefficient: 2.62
Solvent content (%): 53.1
Ligand: 2-({2-fluoro-4-[(2-fluoro-3-nitrobenzyl)sulfonyl]phenyl}sulfanyl)-5-methoxy-N-(3-methyl-1H-pyrazol-5-yl)-6-(morpholin-4-yl)pyrimidin-4-amine (4J7)
Ligand formula: C26 H25 F2 N7 O6 S2
Ligand molecular weight: 633.647
Ligand SMILES: Cc1cc([nH]n1)Nc2c(c(nc(n2)Sc3ccc(cc3F)S(=O)(=O)Cc4cccc(c4F)[N+](=O)[O-])N5CCOCC5)OC
Ligand InChI: InChI=1S/C26H25F2N7O6S2/c1-15-12-21(33-32-15)29-24-23(40-2)25(34-8-10-41-11-9-34)31-26(30-24)42-20-7-6-17(13-18(20)27)43(38,39)14-16-4-3-5-19(22(16)28)35(36)37/h3-7,12-13H,8-11,14H2,1-2H3,(H2,29,30,31,32,33)
Release date: 2015-06-17
Crystal structure of the R64M mutant of Bauhinia Bauhinioides Kallikrein Inhibitor complexed with Human Kallikrein 4 (PDB entry 7JQN)
Macromolecule: Kallikrein-4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 223 residues
Sequence: IINGEDCSPHSQPWQAALVMENELFCSGVLVHPQWVLSAAHCFQNSYTIGLGLHSLEADQEPGSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCPTAGNSCLVSGWGLLANGRMPTVLQCVNVSVVSEEVCSKLYDPLYHPSMFCAGGGQDQKDSCNGDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCKFTEWIEKTVQA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1221
R free: 0.1613
Average B factor: 26.675
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 2.0 Ammonium Sulfate, 2%PEG400, 10mM CdCl2 pH 7.5
Matthews coefficient: 3.23
Solvent content (%): 61.97
Ligand: NONAETHYLENE GLYCOL (2PE)
Ligand formula: C18 H38 O10
Ligand molecular weight: 414.488
Ligand SMILES: C(COCCOCCOCCOCCOCCOCCOCCOCCO)O
Ligand InChI: InChI=1S/C18H38O10/c19-1-3-21-5-7-23-9-11-25-13-15-27-17-18-28-16-14-26-12-10-24-8-6-22-4-2-20/h19-20H,1-18H2
Release date: 2021-07-21
Human DNA Pol eta S113A with dA-ended primer and dATP: in crystallo reaction for 140 s (PDB entry 7M86)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERAAIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1732
R free: 0.2046
Average B factor: 21.2058
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG 2000 MME,
100 mM MES
Matthews coefficient: 2.09
Solvent content (%): 41.05
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: 2021-06-02
17beta-HSD5 in complex with 4-nitro-2-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}methyl)phenol (PDB entry 4XVD)
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): 2.81
R work: 0.20865
R free: 0.25873
Average B factor: 33.592
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: 2.6
Solvent content (%): 52.67
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