satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of SARS-CoV-2 Alpha variant spike receptor-binding domain complexed with human ACE2 (PDB entry 7EKF)
Macromolecule: Spike protein S1
Type: Protein, polypeptide(L)
Source organism: Severe acute respiratory syndrome coronavirus 2
Sequence length: 229 residues
Sequence: RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTYGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2081
R free: 0.2238
Average B factor: 73.01
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES, pH 6.5, 10% w/v PEG 5000 MME, 12% v/v1-Propanol
Matthews coefficient: 3.28
Solvent content (%): 62.49
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: 2021-11-03
Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n2m3 (PDB entry 5BXO)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 164 residues
Sequence: GSGNSEADRQLLEAAKAGDVETVKKLCTVQSVNCRDIEGRQSTPLHFAAGYNRVSVVEYLLQHGADVHAKDKGGLVPLHNACSYGHYEVAELLVKHGAVVNVADLWKFTPLHEAAAKGKYEICKLLLQHGADPTKKNRDGNTPLDLVKDGDTDIQDLLRGDAAL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.334
R work: 0.17484
R free: 0.20273
Average B factor: 16.322
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M tri-sodium citrate, pH 5.0, 3.2 M ammonium sulfate
Matthews coefficient: 1.85
Solvent content (%): 33.61
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: 2016-06-29
Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site (PDB entry 7BJ1)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.354
Sequence length: 431 residues
Sequence: GSHMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.1715
R free: 0.21
Average B factor: 30.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.25
Crystallization temperature (K): 293
Crystal growth procedure: Protein: 50 mM Tris, 150 mM NaCl, 1 mM (S)-diperodon, 10% DMSO, pH 8.0; reservoir: 100 mM Tris, 50 mM magnesium acetate, 11% PEG3350, pH 8.25
Matthews coefficient: 2.18
Solvent content (%): 43.62
Ligand: S-ADENOSYLMETHIONINE (SAM)
Ligand formula: C15 H22 N6 O5 S
Ligand molecular weight: 398.437
Ligand SMILES: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Ligand InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
Release date: 2021-03-03
Crystal structure of primase iron-sulfur domain (266-457) (PDB entry 6DHW)
Macromolecule: DNA primase large subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 192 residues
Sequence: GNVGKISLDQIDLLSTKSFPPCMRQLHKALRENHHLRHGGRMQYGLFLKGIGLTLEQALQFWKQEFIKGKMDPDKFDKGYSYNIRHSFGKEGKRTDYTPFSCLKIILSNPPSQGDYHGCPFRHSDPELLKQKLQSYKISPGGISQILDLVKGTHYQVACQKYFEMIHNVDDCGFSLNHPNQFFCESQRILNG
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.013
R work: 0.1806
R free: 0.2113
Average B factor: 38.8875
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 289
Crystal growth procedure: 100 mM TRIS-HCl pH 8.5, 400 mM LiSO4, 18% PEG3350
Matthews coefficient: 2.64
Solvent content (%): 53.33
Ligand: IRON/SULFUR CLUSTER (SF4)
Ligand formula: Fe4 S4
Ligand molecular weight: 351.64
Ligand SMILES: [S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
Ligand InChI: InChI=1S/4Fe.4S
Release date: 2018-12-19
XChem fragment screen -- CRYSTAL STRUCTURE OF THE BROMODOMAIN OF THE HUMAN ATAD2 in complex with N13475a (PDB entry 5R4V)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYRTVIKEPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.1327
R free: 0.1526
Average B factor: 19.496
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 2.2M ammonium sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 4.2
Solvent content (%): 70.7
Ligand: [4-(cyclopropanecarbonyl)piperazin-1-yl](furan-2-yl)methanone (JMM)
Ligand formula: C13 H16 N2 O3
Ligand molecular weight: 248.278
Ligand SMILES: c1cc(oc1)C(=O)N2CCN(CC2)C(=O)C3CC3
Ligand InChI: InChI=1S/C13H16N2O3/c16-12(10-3-4-10)14-5-7-15(8-6-14)13(17)11-2-1-9-18-11/h1-2,9-10H,3-8H2
Release date: 2020-05-13
Structure of CHK1 10-pt. mutant complex with pyrrolopyrimidine LRRK2 inhibitor (PDB entry 5OP7)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1658
R free: 0.2154
Average B factor: 36.629
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
Matthews coefficient: 2.31
Solvent content (%): 46.68
Ligand: [4-[[5-chloranyl-4-(methylamino)-7~{H}-pyrrolo[2,3-d]pyrimidin-2-yl]amino]-3-methoxy-phenyl]-morpholin-4-yl-methanone (A1K)
Ligand formula: C19 H21 Cl N6 O3
Ligand molecular weight: 416.861
Ligand SMILES: CNc1c2c(c[nH]c2nc(n1)Nc3ccc(cc3OC)C(=O)N4CCOCC4)Cl
Ligand InChI: InChI=1S/C19H21ClN6O3/c1-21-16-15-12(20)10-22-17(15)25-19(24-16)23-13-4-3-11(9-14(13)28-2)18(27)26-5-7-29-8-6-26/h3-4,9-10H,5-8H2,1-2H3,(H3,21,22,23,24,25)
Release date: 2017-10-25
Crystal Structure of Shp2 E76K GOF Mutant in complex with SHP099 (PDB entry 6CRG)
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: GMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAKLVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.196
R free: 0.25
Average B factor: 63.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M Tris pH 8.5, 30% PEG 4000, and 0.2 M LiSO4
Matthews coefficient: 2.23
Solvent content (%): 44.81
Ligand: 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine (5OD)
Ligand formula: C16 H19 Cl2 N5
Ligand molecular weight: 352.262
Ligand SMILES: CC1(CCN(CC1)c2cnc(c(n2)N)c3cccc(c3Cl)Cl)N
Ligand InChI: InChI=1S/C16H19Cl2N5/c1-16(20)5-7-23(8-6-16)12-9-21-14(15(19)22-12)10-3-2-4-11(17)13(10)18/h2-4,9H,5-8,20H2,1H3,(H2,19,22)
Release date: 2018-11-07
Closed structure of inactive SHP2 mutant C459E (PDB entry 6CMP)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 532 residues
Sequence: GSGMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHESAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.2012
R free: 0.2306
Average B factor: 34.52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 200 mM lithium nitrate, 20% PEG 3,350
Matthews coefficient: 2.16
Solvent content (%): 39.04
Release date: 2018-11-14
Crystal structure of a DNA repair complex ASCC3-ASCC2 (PDB entry 6YXQ)
Macromolecule: Activating signal cointegrator 1 complex subunit 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 211 residues
Sequence: GAEFMALPRLTGALRSFSNVTKQDNYNEEVADLKIKRSKLHEQVLDLGLTWKKIIKFLNEKLEKSKMQSINEDLKDILHAAKQIVGTDNGREAIESGAAFLFMTFHLKDSVGHKETKAIKQMFGPFPSSSATAACNATNRIISHFSQDDLTALVQMTEKEHGDRVFFGKNLAFSFDMHDLDHFDELPINGETQKTISLDYKKFLNEHLQEA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2044
R free: 0.2474
Average B factor: 96.04
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: MES-NaOH, pH 6.5, polyethylene glycol 3350, 2-methyl-2,4-pentanediol and methanol
Matthews coefficient: 2.91
Solvent content (%): 57.79
Release date: 2020-09-30
IRAK4 in complex with Compound 1 (PDB entry 5K75)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.03
R work: 0.239
R free: 0.253
Average B factor: 64.42
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.5 ammonium sulfate, 0.1 M Hepes pH 7.2
Matthews coefficient: 2.69
Solvent content (%): 54.31
Ligand: ~{N}1-(7,8-dihydro-6~{H}-cyclopenta[2,3]thieno[2,4-~{c}]pyrimidin-1-yl)-~{N}4,~{N}4-dimethyl-cyclohexane-1,4-diamine (6QX)
Ligand formula: C17 H24 N4 S
Ligand molecular weight: 316.464
Ligand SMILES: CN(C)C1CCC(CC1)Nc2c3c4c(sc3ncn2)CCC4
Ligand InChI: InChI=1S/C17H24N4S/c1-21(2)12-8-6-11(7-9-12)20-16-15-13-4-3-5-14(13)22-17(15)19-10-18-16/h10-12H,3-9H2,1-2H3,(H,18,19,20)/t11-,12-
Release date: 2017-12-06
The crystal structure of FGFR4 kinase domain in complex with N-(5-cyano-4-((2-methoxyethyl)amino)pyridin-2-yl)-7-(2,2,2-trifluoroacetyl)-3,4-dihydro-1,8-naphthyridine-1(2H)-carboxamide (PDB entry 7VJL)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 301 residues
Sequence: DLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDRVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.90017299719
R work: 0.204653382216
R free: 0.273007589253
Average B factor: 51.90497332
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.5m NH4H2PO4
Matthews coefficient: 2.43
Solvent content (%): 49.37
Ligand: N-[5-(aminomethyl)-4-(2-methoxyethylamino)pyridin-2-yl]-7-[2,2,2-tris(fluoranyl)ethanoyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide (7IF)
Ligand formula: C20 H23 F3 N6 O3
Ligand molecular weight: 452.43
Ligand SMILES: COCCNc1cc(ncc1CN)NC(=O)N2CCCc3c2nc(cc3)C(=O)C(F)(F)F
Ligand InChI: InChI=1S/C20H23F3N6O3/c1-32-8-6-25-15-9-16(26-11-13(15)10-24)28-19(31)29-7-2-3-12-4-5-14(27-18(12)29)17(30)20(21,22)23/h4-5,9,11H,2-3,6-8,10,24H2,1H3,(H2,25,26,28,31)
Release date: 2022-02-23
Structure of human PARG complexed with JA2-4 (PDB entry 6O9X)
Macromolecule: Poly(ADP-ribose) glycohydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.143
Sequence length: 533 residues
Sequence: GPHMSPDKKWLGTPIEEMRRMPRCGIRLPLLRPSANHTVTIRVDLLRAGEVPKPFPTHYKDLWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLKDAILKYNVAYSKKWDFTALIDFWDKVLEEAEAQHLYQSILPDMVKIALCLPNICTQPIPLLAAAMNHSITMSQEQIASLLANAFFCTFPRRNAKMKSEYSSYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTAAAPTGLVTFTRQSLEDFPEWERCEKPLTRLHVTYEGTIEENGQGMLQVDFANRFVGGGVTSAGLVQEEIRFLINPELIISRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWSRSHEDGSERDDWQRRCTEIVAIDALHFRRYLDQFVPEKMRRELNKAYCGFLRPGVSSENLSAVATGNWGCGAFGGDARLKALIQILAAAAAERDVVYFTFGDSELMRDIYSMHIFLTERKLTVGDVYKLLLRYYNEECRNCSTPGPDIKLYPFIYHAVESCAETADHSGQRTGT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.15577
R free: 0.19316
Average B factor: 25.498
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% (w/v) PEG 3350, 0.1 M PCTP pH 7.5 and 0.15 M MgCl2
Matthews coefficient: 2.22
Solvent content (%): 44.7
Ligand: 1,3-dimethyl-8-{[2-(pyrrolidin-1-yl)ethyl]sulfanyl}-6-sulfanylidene-1,3,6,9-tetrahydro-2H-purin-2-one (M0S)
Ligand formula: C13 H19 N5 O S2
Ligand molecular weight: 325.453
Ligand SMILES: CN1c2c(nc([nH]2)SCCN3CCCC3)C(=S)N(C1=O)C
Ligand InChI: InChI=1S/C13H19N5OS2/c1-16-10-9(11(20)17(2)13(16)19)14-12(15-10)21-8-7-18-5-3-4-6-18/h3-8H2,1-2H3,(H,14,15)
Release date: 2019-12-25
Crystal structure of the human METTL3-METTL14 complex bound to Compound 1/Adenosine (DHU_M3M_023) (PDB entry 6TTP)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 580 residues
Sequence: MSDTWSSIQAHKKQLDSLRERLQRRRKQDSGHLDLRNPEAALSPTFRSDSPVPTAPTSGGPKPSTASAVPELATDPELEKKLLHHLSDLALTLPTDAVSICLAISTPDAPATQDGVESLLQKFAAQELIEVKRGLLQDDAHPTLVTYADHSKLSAMMGAVAEKKGPGEVAGTVTGQKRRAEQDSTTVAAFASSLVSGLNSSASEPAKEPAKKSRKHAASDVDLEIESLLNQQSTKEQQSKKVSQEILELLNTTTAKEQSIVEKFRSRGRAQVQEFCDYGTKEECMKASDADRPCRKLHFRRIINKHTDESLGDCSFLNTCFHMDTCKYVHYEIDACMDSEAPGSKDHTPSQELALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1932
R free: 0.2274
Average B factor: 44.38
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 25% PEG 3350, 200 mM Magnesium acetate
Ligand: ADENOSINE (ADN)
Ligand formula: C10 H13 N5 O4
Ligand molecular weight: 267.241
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
Ligand InChI: InChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
Release date: 2020-03-04
TRIM7 in complex with C-terminal peptide of NSP12 (PDB entry 7X6Z)
Macromolecule: E3 ubiquitin-protein ligase TRIM7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 174 residues
Sequence: KEEKVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGRHHWEVEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCGHLSRVRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1434
R free: 0.1722
Average B factor: 22.16
Crystallization method: LIQUID DIFFUSION
Crystallization temperature (K): 291.15
Crystal growth procedure: DL-Malic acid, PEG3350
Matthews coefficient: 2.42
Solvent content (%): 49.11
Release date: 2022-08-10
The crystal structure of CASK/Mint1 complex (PDB entry 6KMH)
Macromolecule: Peripheral plasma membrane protein CASK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 325 residues
Sequence: GPGSEFMADDDVLFEDVYELCEVIGKGPFSVVRRCINRETGQQFAVKIVDVAKFTSSPGLSTEDLKREASICHMLKHPHIVELLETYSSDGMLYMVFEFMDGADLCFEIVKRADAGFVYSEAVASHYMRQILEALRYCHDNNIIHRDVKPHCVLLASKENSAPVKLGGFGVAIQLGESGLVAGGRVGTPHFMAPEVVKREPYGKPVDVWGCGVILFILLSGCLPFYGTKERLFEGIIKGKYKMNPRQWSHISESAKDLVRRMLMLDPAERITVYEALNHPWLKERDRYAYKIHLPETVEQLRKFNARRKLKGAVLAAVSSHKFNS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1882
R free: 0.2241
Average B factor: 46.9959
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.2M KI, 20% PEG 3350, pH 7.0
Matthews coefficient: 2.64
Solvent content (%): 53.42
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2020-08-05
DNA polymerase beta imidodiphosphate reactant complex (PDB entry 5UGN)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACGGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.997
R work: 0.181
R free: 0.2432
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM imidazole, 350 mM sodium chloride, 17% PEG3350
Matthews coefficient: 2.23
Solvent content (%): 44.8
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: 2017-07-26
Crystal structure of zebrafish Sirtuin 5 in complex with 3-(benzylthio)succinyl-CPS1 peptide (PDB entry 6FKY)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Danio rerio
EC number: 3.5.1
Sequence length: 284 residues
Sequence: GIDPFTKMTRPSSDLTAFREHFAKAKHIAIITGAGVSAESGVPTFRGPGGFWRKWQAQDLATPEAFSRDPSLVWEFYHYRREVMRSKMPNPAHLAIAECEARLGQQGRSVVIITQNIDELHHRAGSKHVYEIHGSLFKTRCMSCGEVKANHKSPICPALDGKGAPDPNTKEARIPVELLPRCERKSCNGLLRPHVVWFGETLDSDILTAVERELEKCDLCLVVGTSSIVYPAAMFAPQVASRGVPVAEFNMECTPATQRFKYHFEGPCGSTLPPALERHESEAV
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.98
R work: 0.19785
R free: 0.27485
Average B factor: 67.667
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES pH 7.4, 20% PEG3350
Matthews coefficient: 2.63
Solvent content (%): 53.24
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: 2018-03-21
Crystal Structure of human phosphodiesterase 10 in complex with 4-N-ethyl-5-[3-(trifluoromethyl)phenyl]-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine (PDB entry 5SJJ)
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): 2.1
R work: 0.1736
R free: 0.2396
Average B factor: 37.177
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: 2.69
Solvent content (%): 54.19
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
SHP2 SH2 domain in complex with GAB1 peptide (PDB entry 4QSY)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 108 residues
Sequence: GSMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2
R free: 0.2291
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 25% PEG3000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Matthews coefficient: 2.57
Solvent content (%): 52.2
Release date: 2015-07-08