satarupa22/MacromolecularLigandDB huggingface dataset:
Structural Investigations of the Substrate Specificity of Human O-GlcNAcase (PDB entry 5VVV)
Macromolecule: Protein O-GlcNAcase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.169
Sequence length: 504 residues
Sequence: HFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDNIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRKDVVMTDSEDSTVSIQIKLENEGSDEDIETDVLYSPQMALKLALTEWLQEFGVPHQYSSRGGGGSGGGGSVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSVVSVNCKGKDSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRSHSSAQFLIGDQEPWAFRGGLAGEFQRLLPIDGANDLFFQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.19603
R free: 0.25684
Average B factor: 74.527
Crystallization method: EVAPORATION
Crystallization temperature (K): 293
Crystal growth procedure: 0.024 M ammonium citrate tribasic (pH 7.0), 0.015 M MES monohydrate, 0.096 M potassium thiocyanate, 0.25 M Sodium acetate trihydrate, 0.037 M imidazole, 0.002 M zinc sulfate heptahydrate, 9.6 % w/v polyethylene glycol 3,350, 2.4 % w/v polyethylene glycol monomethyl ether 2,000, and 4% w/v polyethylene glycol monomethyl ether 550
Matthews coefficient: 2.76
Solvent content (%): 55.4
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: 2017-09-27
Crystal structure of haspin (GSG2) in complex with macrocycle ODS2004093 (PDB entry 6Z5E)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1572
R free: 0.1831
Average B factor: 18.394
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 60%(v/v) MPD, 0.1M SPG pH 6.0
Matthews coefficient: 3.07
Solvent content (%): 59.99
Ligand: SUCCINIC ACID (SIN)
Ligand formula: C4 H6 O4
Ligand molecular weight: 118.088
Ligand SMILES: C(CC(=O)O)C(=O)O
Ligand InChI: InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)
Release date: 2020-06-03
Human carboanhydrase F131C_C206S double mutant in complex with SA-2 (PDB entry 5T71)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDCGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLESVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.14807
R free: 0.17137
Average B factor: 15.292
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 3 M (NH4)2SO4, 50 mM Tris-HCl
Matthews coefficient: 2.11
Solvent content (%): 41.67
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: 2017-09-06
LSD1-S2157 N5 adduct model (PDB entry 6KGP)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1731
R free: 0.2043
Average B factor: 62.58
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10% PEG3350
Matthews coefficient: 3.75
Solvent content (%): 67.17
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: 2020-03-25
Structure of ULK1 bound to a selective inhibitor (PDB entry 5CI7)
Macromolecule: Serine/threonine-protein kinase ULK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 287 residues
Sequence: GGGSMEPGRGGTETVGKFEFSRKDLIGHGAFAVVFKGRHRAAHDLEVAVKCINKKNLAKSQTLLGKEIKILKELKHENIVALYDFQEMANSVYLVMEYCNGGDLADYLHAMRTLSEDTIRLFLQQIAGAMRLLHSKGIIHRDLKPQNILLSNPAGRRANPNSIRVKIADFGFARYLQSNMMAATLCGSPMYMAPEVIMSQHYDGKADLWSIGTIVYQCLTGKAPFQASSPQDLRLFYEKNKTLVPTIPRETSAPLRQLLLALLQRNHKDRMDFDEFFHHPFLDASPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1688
R free: 0.2069
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 298
Crystal growth procedure: 1.55 M sodium malonate pH 7.0, 0.35 M sodium malonate pH 5.0
Matthews coefficient: 2.02
Solvent content (%): 38.99
Ligand: N-[3-({4-[(3-aminopropyl)amino]-5-iodopyrimidin-2-yl}amino)phenyl]pyrrolidine-1-carboxamide (51W)
Ligand formula: C18 H24 I N7 O
Ligand molecular weight: 481.334
Ligand SMILES: c1cc(cc(c1)NC(=O)N2CCCC2)Nc3ncc(c(n3)NCCCN)I
Ligand InChI: InChI=1S/C18H24IN7O/c19-15-12-22-17(25-16(15)21-8-4-7-20)23-13-5-3-6-14(11-13)24-18(27)26-9-1-2-10-26/h3,5-6,11-12H,1-2,4,7-10,20H2,(H,24,27)(H2,21,22,23,25)
Release date: 2015-08-26
New Irreversible a-l-Iduronidase Inhibitors and Activity-Based Probes (PDB entry 6I6X)
Macromolecule: Alpha-L-iduronidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.76
Sequence length: 627 residues
Sequence: EAPHLVQVDAARALWPLRRFWRSTGFCPPLPHSQADPYVLSWDQQLNLAYVGAVPHRGIKQVRTHWLLELVTTRGSTGRGLSYNFTHLDGYLDLLRENQLLPGFELMGSASGHFTDFEDKQQVFEWKDLVSSLARRYIGRYGLAHVSKWNFETWNEPDHHDFDNVSMTMQGFLNYYDACSEGLRAASPALRLGGPGDSFHTPPRSPLSWGLLRHCHDGTNFFTGEAGVRLDYISLHRKGARSSISILEQEKVVAQQIRQLFPKFADTPIYNDEADPLVGWSLPQPWRADVTYAAMVVKVIAQHQNLLLANTTSAFPYALLSNDNAFLSYHPHPFAQRTLTARFQVNNTRPPHVQLLRKPVLTAMGLLALLDEEQLWAEVSQAGTVLDSNHTVGVLASAHRPQGPADAWRAAVLIYASDDTRAHPNRSVAVTLRLRGVPPGPGLVYVTRYLDNGLCSPDGEWRRLGRPVFPTAEQFRRMRAAEDPVAAAPRPLPAGGRLTLRPALRLPSLLLVHVCARPEKPPGQVTRLRALPLTQGQLVLVWSDEHVGSKCLWTYEIQFSQDGKAYTPVSRKPSTFNLFVFSPDTGAVSGSYRVRALDYWARPGPFSDPVPYLEVPVPRGPPSPGNP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.39
R work: 0.19063
R free: 0.21605
Average B factor: 41.978
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 7.5, 0.26 M Sodium potassium tartrate, 20 % w/v PEG3350
Matthews coefficient: 2.11
Solvent content (%): 41.6
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: 2018-12-05
Crystal structure of EGFR_TMX in complex with covalently bound fragment 10 (PDB entry 8HV8)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGSLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2315
R free: 0.28257
Average B factor: 40.424
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M TRIS pH 8.5, 0.15M Sodium citrate, 25%PEG400
Matthews coefficient: 3.32
Solvent content (%): 62.9
Ligand: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL (PE5)
Ligand formula: C18 H38 O9
Ligand molecular weight: 398.489
Ligand SMILES: CCOCCOCCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C18H38O9/c1-2-20-5-6-22-9-10-24-13-14-26-17-18-27-16-15-25-12-11-23-8-7-21-4-3-19/h19H,2-18H2,1H3
Release date: 2023-12-13
Structure of Serine-Threonine kinase STK25 in complex with compound (PDB entry 7Z4V)
Macromolecule: Serine/threonine-protein kinase 25
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: GSMAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGIDNHTKEVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHRDIKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIELAKGEPPNSDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFVEACLNKDPRFRPTAKELLKHKFITRYTKKTSFLTELIDRYKRWKSEGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.644
R work: 0.2451
R free: 0.2834
Average B factor: 30.74
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 22 % PEG 3350, 0.1 M Bis-tris propane pH 8.5, 0.2 M Potassium citrate, 10 % ethylene glycol
Matthews coefficient: 2.5
Solvent content (%): 50.84
Ligand: ~{N}-(5-~{tert}-butyl-1~{H}-pyrazol-3-yl)-4-pyrrolidin-1-ylsulfonyl-benzamide (IB5)
Ligand formula: C18 H24 N4 O3 S
Ligand molecular weight: 376.473
Ligand SMILES: CC(C)(C)c1cc(n[nH]1)NC(=O)c2ccc(cc2)S(=O)(=O)N3CCCC3
Ligand InChI: InChI=1S/C18H24N4O3S/c1-18(2,3)15-12-16(21-20-15)19-17(23)13-6-8-14(9-7-13)26(24,25)22-10-4-5-11-22/h6-9,12H,4-5,10-11H2,1-3H3,(H2,19,20,21,23)
Release date: 2022-04-06
Crystal structure of the titin domain Fn3-90 (PDB entry 8OTY)
Macromolecule: Titin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 104 residues
Sequence: GSSDSPSAPVNLTIREVKKDSVTLSWEPPLIDGGAKITNYIVEKRETTRKAYATITNNCTKTTFRIENLQEGCSYYFRVLASNEYGIGLPAETTEPVKVSEPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2009
R free: 0.2508
Average B factor: 25.36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30mM HEPES pH 7.5
150mM NaCl
1mM DTT
100mM Sodium acetate
200mM CaCl
20% w/v PEG6000
Matthews coefficient: 1.88
Solvent content (%): 34.48
Release date: 2023-08-23
Crystal structure of human JMJD2A in complex with compound 43 (PDB entry 5A7N)
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): 2.39
R work: 0.1828
R free: 0.2445
Crystallization pH: 7.5
Crystal growth procedure: 22% PEG3350 -- 0.1M BIS-TRIS PH 7.5 -- 0.25M AMMONIUM SULFATE
Matthews coefficient: 2.72
Solvent content (%): 54.76
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
Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP504 (PDB entry 6BMV)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.053
R work: 0.174
R free: 0.223
Average B factor: 44.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG3350, 200MM AMMONIUM PHOSPHATE
Matthews coefficient: 2.31
Solvent content (%): 46.78
Ligand: 3-{4-[(2-chlorophenyl)methyl]-5-oxo-4,5-dihydro[1,2,4]triazolo[4,3-a]quinazolin-1-yl}-4-hydroxybenzoic acid (DZS)
Ligand formula: C23 H15 Cl N4 O4
Ligand molecular weight: 446.843
Ligand SMILES: c1ccc(c(c1)CN2c3nnc(n3-c4ccccc4C2=O)c5cc(ccc5O)C(=O)O)Cl
Ligand InChI: InChI=1S/C23H15ClN4O4/c24-17-7-3-1-5-14(17)12-27-21(30)15-6-2-4-8-18(15)28-20(25-26-23(27)28)16-11-13(22(31)32)9-10-19(16)29/h1-11,29H,12H2,(H,31,32)
Release date: 2018-01-17
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z1699011516 (PDB entry 5QOV)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1948
R free: 0.2396
Average B factor: 33.456
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.48
Solvent content (%): 50.45
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: 2019-05-08
Human DNA Ligase 1(E346A/E592A) Bound to a bulged DNA substrate (PDB entry 7KR3)
Macromolecule: DNA ligase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.5.1.1
Sequence length: 647 residues
Sequence: SNDMDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.778
R work: 0.1932
R free: 0.2394
Average B factor: 87.7862
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, 150 mM lithium acetate, 10% (w/v) polyethylene glycol 3350
Matthews coefficient: 2.6
Solvent content (%): 52.69
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2021-02-03
Carbonic Anhydrase II Complexed with 2-((2-Cyanoethyl)(phenethyl)amino)-N-phenethyl-N-(4-sulfamoylphenethyl)acetamide (PDB entry 6WQ4)
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): 1.35
R work: 0.1539
R free: 0.1724
Average B factor: 16.1773
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M sodium citrate and 50mM Tris at pH 7.8
Matthews coefficient: 2.1
Solvent content (%): 41.49
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2020-06-24
Crystal Structure of Factor VIIa in complex with N-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]pentanamide (PDB entry 5PB6)
Macromolecule: Coagulation factor VII heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 254 residues
Sequence: IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1876
R free: 0.2105
Average B factor: 21.801
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: 3.76
Solvent content (%): 67.27
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: 2017-06-21
Crystal structure of FGFR3 in complex with pyrimidine derivative (PDB entry 6LVM)
Macromolecule: Fibroblast growth factor receptor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 313 residues
Sequence: GSHMLAGVSEYELPEDPKWEFPRDKLTLGKPLGEGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNIINLLGACTQGGPLYVLVEYAAKGNLREFLRARRPPGLDYSFDTCKPPEEQLTFKDLVSCAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSTDE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.2074
R free: 0.2789
Average B factor: 56.476
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 296
Crystal growth procedure: Citric Acid, PEG 8000
Matthews coefficient: 2.27
Solvent content (%): 45.79
Ligand: 2-[[5-[2-(3,5-dimethoxyphenyl)ethyl]-2-[[3-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]amino]pyrimidin-4-yl]amino]-N-ethyl-benzenesulfonamide (EVR)
Ligand formula: C39 H52 N8 O5 S
Ligand molecular weight: 744.946
Ligand SMILES: CCNS(=O)(=O)c1ccccc1Nc2c(cnc(n2)Nc3ccc(c(c3)OC)N4CCC(CC4)N5CCN(CC5)C)CCc6cc(cc(c6)OC)OC
Ligand InChI: InChI=1S/C39H52N8O5S/c1-6-41-53(48,49)37-10-8-7-9-34(37)43-38-29(12-11-28-23-32(50-3)26-33(24-28)51-4)27-40-39(44-38)42-30-13-14-35(36(25-30)52-5)47-17-15-31(16-18-47)46-21-19-45(2)20-22-46/h7-10,13-14,23-27,31,41H,6,11-12,15-22H2,1-5H3,(H2,40,42,43,44)
Release date: 2020-04-08
Crystal structure of human Casein Kinase II subunit alpha (CK2a1) in complex with Leucettinib-92 (PDB entry 8P05)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 338 residues
Sequence: SMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.20883
R free: 0.25499
Average B factor: 60.478
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M ammonia sulphate 0.1 M bis-tris pH 5.5 23-26% PEG 3350
Matthews coefficient: 3.13
Solvent content (%): 60.65
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: 2023-05-17
Abl2 SH3 (PDB entry 5NP3)
Macromolecule: Abelson tyrosine-protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 61 residues
Sequence: GSHMNLFVALYDFVASGDNTLSITKGEKLRVLGYNQNGEWSEVRSKNGQGWVPSNYITPVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2006
R free: 0.2344
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 1.8 M di-sodium-DL-malate
Matthews coefficient: 1.86
Solvent content (%): 33.86
Release date: 2018-05-16