satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-2-methyl-N-(2-phenylimidazo[1,2-a]pyrimidin-7-yl)pyrazole-3-carboxamide (PDB entry 5SIP)
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: 0.1906
R free: 0.2265
Average B factor: 41.422
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: 2.63
Solvent content (%): 53.32
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 Hexokinase 2 with cmpd 27, a 2-amido-6-benzenesulfonamide glucosamine (PDB entry 5HFU)
Macromolecule: Hexokinase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.1
Sequence length: 923 residues
Sequence: MGSSHHHHHHSSGLENLYFQGSDQVQKVDQYLYHMRLSDETLLEISKRFRKEMEKGLGATTHPTAAVKMLPTFVRSTPDGTEHGEFLALDLGGTNFRVLWVKVTDNGLQKVEMENQIYAIPEDIMRGSGTQLFDHIAECLANFMDKLQIKDKKLPLGFTFSFPCHQTKLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDTVGTMMTCGYDDHNCEIGLIVGTGSNACYMEEMRHIDMVEGDEGRMCINMEWGAFGDDGSLNDIRTEFDQEIDMGSLNPGKQLFEKMISGMYMGELVRLILVKMAKEELLFGGKLSPELLNTGRFETKDISDIEGEKDGIRKAREVLMRLGLDPTQEDCVATHRICQIVSTRSASLCAATLAAVLQRIKENKGEERLRSTIGVDGSVYKKHPHFAKRLHKTVRRLVPGCDVRFLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEHLQLSHDQLLEVKRRMKVEMERGLSKETHASAPVKMLPTYVCATPDGTEKGDFLALDLGGTNFRVLLVRVRNGKWGGVEMHNKIYAIPQEVMHGTGDELFDHIVQCIADFLEYMGMKGVSLPLGFTFSFPCQQNSLDESILLKWTKGFKASGCEGEDVVTLLKEAIHRREEFDLDVVAVVNDTVGTMMTCGFEDPHCEVGLIVGTGSNACYMEEMRNVELVEGEEGRMCVNMEWGAFGDNGCLDDFRTEFDVAVDELSLNPGKQRFEKMISGMYLGEIVRNILIDFTKRGLLFRGRISERLKTRGIFETKFLSQIESDCLALLQVRAILQHLGLESTCDDSIIVKEVCTVVARRAAQLCGAGMAAVVDRIRENRGLDALKVTVGVDGTLYKLHPHFAKVMHETVKDLAPKCDVSFLQSEDGSGKGAALITAVACRIREAGQR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.923
R work: 0.1824
R free: 0.252
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6
Crystallization temperature (K): 296
Crystal growth procedure: protein: 10mgs/mL in 50mM TrisHCL pH = 7.5, 250mM NaCl, 2mM DTT, 2mM MgCl2
Well solution: 0.1M Na Citrate pH = 6, 16 % PEG3350, 10 % Ethylene glycol
Cryo: 20 % ethylene glycol in well
Matthews coefficient: 2.82
Solvent content (%): 56.35
Ligand: ~{N}-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-[[(4-cyanophenyl)sulfonylamino]methyl]-2,4,5-tris(oxidanyl)oxan-3-yl]-3-phenyl-benzamide (603)
Ligand formula: C26 H25 N3 O7 S
Ligand molecular weight: 523.558
Ligand SMILES: c1ccc(cc1)c2cccc(c2)C(=O)NC3C(C(C(OC3O)CNS(=O)(=O)c4ccc(cc4)C#N)O)O
Ligand InChI: InChI=1S/C26H25N3O7S/c27-14-16-9-11-20(12-10-16)37(34,35)28-15-21-23(30)24(31)22(26(33)36-21)29-25(32)19-8-4-7-18(13-19)17-5-2-1-3-6-17/h1-13,21-24,26,28,30-31,33H,15H2,(H,29,32)/t21-,22-,23-,24-,26+/m1/s1
Release date: 2016-03-30
c-KIT kinase domain in complex with avapritinib derivative 4 (PDB entry 8PQA)
Macromolecule: Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: GSMPMYEVQWKVVEESNGNNYSYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAQGLIKSDAAMTVAVKMLKPSAHSTEREALMSELKVLSYLGNHENIVNLLGACTHGGPTLVITEYCCYGDLLNFLRRKRDEFVPYKVAPEDLYKDFLTLEHLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGNITKICDFGLARDIKNDSNYVDKGNARLPVKWMAPESIFNSVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMSSPEYAPAEMYDIMKTCWDADPDKRPTFKQIVQDIEKQISESTNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1877
R free: 0.214
Average B factor: 45.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 3 mg/mL, 23% PEG3350, 150 mM Na2-tartrate
Matthews coefficient: 1.93
Solvent content (%): 36.21
Ligand: 6-(1-methylpyrazol-4-yl)-4-(4-pyrimidin-2-ylpiperazin-1-yl)pyrrolo[2,1-f][1,2,4]triazine (98A)
Ligand formula: C18 H19 N9
Ligand molecular weight: 361.404
Ligand SMILES: Cn1cc(cn1)c2cc3c(ncnn3c2)N4CCN(CC4)c5ncccn5
Ligand InChI: InChI=1S/C18H19N9/c1-24-11-15(10-22-24)14-9-16-17(21-13-23-27(16)12-14)25-5-7-26(8-6-25)18-19-3-2-4-20-18/h2-4,9-13H,5-8H2,1H3
Release date: 2023-12-27
Structure of human RTCB (PDB entry 8BTT)
Macromolecule: RNA-splicing ligase RtcB homolog
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.5.1.8
Sequence length: 530 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMSRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELRNACRGGGVGGFLPAMKQIGNVAALPGIVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDINCGVRLLRTNLDESDVQPVKEQLAQAMFDHIPVGVGSKGVIPMNAKDLEEALEMGVDWSLREGYAWAEDKEHCEEYGRMLQADPNKVSARAKKRGLPQLGTLGAGNHYAEIQVVDEIFNEYAAKKMGIDHKGQVCVMIHSGSRGLGHQVATDALVAMEKAMKRDKIIVNDRQLACARIASPEGQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYDVSHNIAKVEQHVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQPVLIGGTMGTCSYVLTGTEQGMTETFGTTCHGAGRALSRAKSRRNLDFQDVLDKLADMGIAIRVASPKLVMEEAPESYKNVTDVVNTCHDAGISKKAIKLRPIAVIKG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1992
R free: 0.2556
Average B factor: 71.34
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293.15
Crystal growth procedure: protein: 125 uM in 25 mM Tris pH 7.5, 200 mM NaCl, 10 % glycerol, 1mM TCEP, 2 mM manganese chloride
reservoir: 0.1 M magnesium chloride, 0.1 M HEPES pH 7.0, 15 % PEG 4000
drop: 800 nl protein + 600 nl reservoir
Matthews coefficient: 2.33
Solvent content (%): 47.28
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: 2023-12-13
RCR E3 ligase E2-Ubiquitin transthiolation intermediate (PDB entry 6T7F)
Macromolecule: E3 ubiquitin-protein ligase MYCBP2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2
Sequence length: 261 residues
Sequence: GPLGSDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVLENRWLGPRITFGFISCPICKNKINHIVLKDLLDPIKELYEDVRRKALMRLEYEGLHKSEAITTPGVRFYNDPAGYAMNRYAYYVCYKCRKAYFGGEARCDAEAGRGDDYDPRELICGACSDVSRAQMCPKHGTDFLEYKCRYCCSVAVFFCFGTTHFCNACHDDFQRMTSIPKEELPHCPAGPKGKQLEGTECPLHVVHPPTGEEFALGCGVCRNAHTF
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.1951
R free: 0.2561
Average B factor: 78.285
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 292
Crystal growth procedure: 0.85 M sodium citrate, 100 mM sodium chloride, 100 mM Tris-HCl pH 8.0
Matthews coefficient: 2.46
Solvent content (%): 50.08
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: 2020-08-05
CATHEPSIN L IN COMPLEX WITH (3S,14E)-19-chloro-N-(1-cyanocyclopropyl)-5-oxo-12,17-dioxa-4-azatricyclo[16.2.2.06,11]docosa-1(21),6(11),7,9,14,18(22),19-heptaene-3-carboxamide (PDB entry 6EZP)
Macromolecule: Cathepsin L1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.15
Sequence length: 220 residues
Sequence: APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.37
R work: 0.21086
R free: 0.23336
Average B factor: 17.595
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 3.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.1 M citrate, 25% PEG3350
Matthews coefficient: 2.4
Solvent content (%): 48.8
Ligand: (3~{S},14~{E})-19-chloranyl-~{N}-(1-cyanocyclopropyl)-5-oxidanylidene-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(21),6(11),7,9,14,18(22),19-heptaene-3-carboxamide (C3E)
Ligand formula: C24 H22 Cl N3 O4
Ligand molecular weight: 451.902
Ligand SMILES: c1ccc2c(c1)C(=O)NC(Cc3ccc(c(c3)Cl)OCC=CCO2)C(=O)NC4(CC4)C#N
Ligand InChI: InChI=1S/C24H22ClN3O4/c25-18-13-16-7-8-21(18)32-12-4-3-11-31-20-6-2-1-5-17(20)22(29)27-19(14-16)23(30)28-24(15-26)9-10-24/h1-8,13,19H,9-12,14H2,(H,27,29)(H,28,30)/b4-3+/t19-/m0/s1
Release date: 2018-04-11
Crystal structure of Werner syndrome helicase (PDB entry 6YHR)
Macromolecule: Werner syndrome ATP-dependent helicase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 585 residues
Sequence: MNEGEEDDDKDFLWPAPNEEQVTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFLGSAQSENVLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKTSSHWEFEGPTIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKASLGIMGTEKCCDNCRSRLDHCYSMDDSEDTSWDFGPQAFKLLSAVDILGEKFGIGLPILFLRGSNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICALTKKGRNWLHKANTESQSLILQANEELCPKKFLLPSSKTVSSGTKEHCYNQAENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1969
R free: 0.2363
Average B factor: 71.05
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 1M Na Acetate, 0.1 M Cacodylate pH 6.5
Matthews coefficient: 2.56
Solvent content (%): 51.91
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2020-04-29
Crystal structure of RhoA mutant L69P complexed with GDP (PDB entry 8GI3)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 196 residues
Sequence: GPLMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRPRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCLVL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.17057
R free: 0.20947
Average B factor: 13.318
Crystallization method: MICROBATCH
Crystallization pH: 5.1
Crystallization temperature (K): 293.2
Crystal growth procedure: 0.2 M Ammonium citrate dibasic (pH 5.1), 20% PEG3350
Matthews coefficient: 2.03
Solvent content (%): 39.5
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2024-03-20
Human Carbonic Anhydrase II in complex with 4-(3-(3-phenoxypropyl)thioureido)benzenesulfonamide (PDB entry 7A6V)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 258 residues
Sequence: HHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.209
R free: 0.2581
Average B factor: 17.657
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 1,5-1,8 M sodium citrate
Matthews coefficient: 2.07
Solvent content (%): 40.66
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: 2021-10-06
Human DNA polymerase eta-DNA ternary mismatch complex:reaction with 10.0 mM Mn2+ for 120s (PDB entry 7U7G)
Macromolecule: DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 12 residues
Sequence: CATTATGACGCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1751
R free: 0.2097
Average B factor: 37.2778
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 10% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.06
Solvent content (%): 40.28
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: 2022-05-04
cCBL TKB domain in complex with pZAP70 peptide (PDB entry 7SIY)
Macromolecule: E3 ubiquitin-protein ligase CBL
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 304 residues
Sequence: PGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.2085
R free: 0.2209
Average B factor: 51.84
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Ammonium formate, 20% PEG3350
Matthews coefficient: 3.46
Solvent content (%): 64.49
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: 2022-11-09
The FK1 domain of FKBP51 in complex with peptide-inhibitor hit DFPFV (PDB entry 7ETV)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 129 residues
Sequence: MGAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1712
R free: 0.1895
Average B factor: 10.744
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 30%-36% PEG 3350, 0.2 M Ammonium Acetate and 0.1 M HEPES pH 7.5
Matthews coefficient: 2.2
Solvent content (%): 44.21
Release date: 2022-02-23
Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain (PDB entry 5KH3)
Macromolecule: Histone deacetylase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 107 residues
Sequence: GSPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1572
R free: 0.1907
Average B factor: 15.362
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 291
Crystal growth procedure: 2M Na-formate, 0.2M Na-acetate pH4.6, 5% ethylene glycol
Matthews coefficient: 2.1
Solvent content (%): 41.38
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2016-07-27
Structure of CHD4 double chromodomains depicts cooperative folding for DNA binding (PDB entry 4O9I)
Macromolecule: Chromodomain-helicase-DNA-binding protein 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 202 residues
Sequence: MAHHHHHHVDDDDKENLYFQMKGKVQKILIWKWGQPPSPTPVPRPPDADPNTPSPKPLEGRPERQFFVKWQGMSYWHCSWVSELQLELHCQVMFRNYQRKNDMDEPPSGDFGGDEEKSRKRKNKDPKFAEMEERFYRYGIKPEWMMIHRILNHSVDKKGHVHYLIKWRDLPYDQASWESEDVEIQDYDLFKQSYWNHRELKK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.21106
R free: 0.26373
Average B factor: 56.179
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M Ammonium citrate, 20% PEG3350, pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2.82
Solvent content (%): 56.43
Release date: 2015-07-08
Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with T-49 (PDB entry 6NJI)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 370 residues
Sequence: MSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQAPAPPLDEQNRDSQGNQVSEFISNTFLDENLYFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.184
R free: 0.23
Average B factor: 50.86
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.14
Crystallization temperature (K): 289
Crystal growth procedure: 5.0MG/ML VCID7620 + 0.5MM T-049
 1MM DTT, 0.1MM ZNCL2, 0.1MM MGCL2 (BATCH 1214023) AGAINST
 OPTIMIZATION MATRIX BASED ON CONDITION MORPHEUS C8, 47.47%V/V
 OF 2X MORPHEUS-PPT4 (FINAL = 11.8% W/V PEG1,000 , 11.8% W/V
 PEG3,350 , 11.8% W/V MPD), 0.03M NPS (SODIUM NITRATE, DISODIUM
 HYDROGEN PHOSPHATE, AMMONIUM SULFATE), 0.1M HEPES PH 7.14,
 CRYO-PROTECTED - DIRECT (ZQV4-6); TRAY ID 236552B5, VAPOR
 DIFFUSION, SITTING DROP, TEMPERATURE 289K
Matthews coefficient: 2.44
Solvent content (%): 49.66
Ligand: 2-(4-{[4-(3-chlorophenyl)-6-ethyl-1,3,5-triazin-2-yl]amino}phenyl)ethan-1-ol (KR4)
Ligand formula: C19 H19 Cl N4 O
Ligand molecular weight: 354.833
Ligand SMILES: CCc1nc(nc(n1)Nc2ccc(cc2)CCO)c3cccc(c3)Cl
Ligand InChI: InChI=1S/C19H19ClN4O/c1-2-17-22-18(14-4-3-5-15(20)12-14)24-19(23-17)21-16-8-6-13(7-9-16)10-11-25/h3-9,12,25H,2,10-11H2,1H3,(H,21,22,23,24)
Release date: 2019-05-08
Crystal structure of Human histone acetytransferas 1 (HAT1) in complex with isobutryl-COA and K12A mutant variant of histone H4 (PDB entry 6VO5)
Macromolecule: Histone acetyltransferase type B catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 324 residues
Sequence: GSKKLAEYKCNTNTAIELKLVRFPEDLENDIRTFFPEYTHQLFGDDETAFGYKGLKILLYYIAGSLSTMFRVEYASKVDENFDCVEADDVEGKIRQIIPPGFCTNTNDFLSLLEKEVDFKPFGTLLHTYSVLSPTGGENFTFQIYKADMTCRGFREYHERLQTFLMWFIETASFIDVDDERWHYFLVFEKYNKDGATLFATVGYMTVYNYYVYPDKTRPRVSQMLILTPFQGQGHGAQLLETVHRYYTEFPTVLDITAEDPSKSYVKLRDFVLVKLCQDLPCFSREKLMQGFNEDMAIEAQQKFKINKQHARRVYEILRLLVTD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1708
R free: 0.1976
Average B factor: 25.604
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG 20K and 0.1M MES pH6.5
Matthews coefficient: 3.04
Solvent content (%): 59.57
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2020-03-11
Human Carbonic Anhydrase II in complex with (R)-1-aminopropan-2-ol (PDB entry 6SDJ)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.02
R work: 0.1283
R free: 0.1396
Average B factor: 13.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate 2.7 M, TRIS 0.1, saturated with para-Chloromercuribenzoic acid
Matthews coefficient: 2.05
Solvent content (%): 39.9
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: 2020-04-15
Crystal structure of human DEAH-box helicase DHX15 in complex with SUGP1 G-patch (PDB entry 8EJM)
Macromolecule: ATP-dependent RNA helicase DHX15
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 686 residues
Sequence: SNMQCINPFTNLPHTPRYYDILKKRLQLPVWEYKDRFTDILVRHQSFVLVGETGSGKTTQIPQWCVEYMRSLPGPKRGVACTQPRRVAAMSVAQRVADEMDVMLGQEVGYSIRFEDCSSAKTILKYMTDGMLLREAMNDPLLERYGVIILDEAHERTLATDILMGVLKEVVRQRSDLKVIVMSATLDAGKFQIYFDNCPLLTIPGRTHPVEIFYTPEPERDYLEAAIRTVIQIHMCEEEEGDLLLFLTGQEEIDEACKRIKREVDDLGPEVGDIKIIPLYSTLPPQQQQRIFEPPPPKKQNGAIGRKVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVTAISKASAQQRAGRAGRTRPGKCFRLYTEKAYKTEMQDNTYPEILRSNLGSVVLQLKKLGIDDLVHFDFMDPPAPETLMRALELLNYLAALNDDGDLTELGSMMAEFPLDPQLAKMVIASCDYNCSNEVLSITAMLSVPQCFVRPTEAKKAADEAKMRFAHIDGDHLTLLNVYHAFKQNHESVQWCYDNFINYRSLMSADNVRQQLSRIMDRFNLPRRSTDFTSRDYYINIRKALVTGYFMQVAHLERTGHYLTVKDNQVVQLHPSTVLDHKPEWVLYNEFVLTTKNYIRTCTDIKPEWLVKIAPQYYDMSNFPQCEAKRQLDRIIAKLQSKEYSQY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1887
R free: 0.2244
Average B factor: 45.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG3350, ammonium sulfate, HEPES buffer
Matthews coefficient: 2.3
Solvent content (%): 46.46
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2022-12-14