satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Human Kallikrein 6 in complex with GSK144 (PDB entry 6QFF)
Macromolecule: Kallikrein-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 222 residues
Sequence: LVHGGPCDKTSHPYQAALYTSGHLLCGGVLIHPLWVLTAAHCKKPNLQVFLGKHNLGQQESSQEQSSVVRAVIHPDYDAASHDQDIMLLRLARPAKLSELIQPLPLERDCSAQTTSCHILGWGKTADGDFPDTIQCAYIHLVSREECEHAYPGQITQNMLCAGDEKYGKDSCQGDSGGPLVCGDHLRGLVSWGNIPCGSKEKPGVYTNVCRYTNWIQKTIQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.186
R free: 0.214
Average B factor: 26.38
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.6
Crystallization temperature (K): 293
Crystal growth procedure: 100mM Tris-HCl pH 8.6, PEG 4000 18-28%
Matthews coefficient: 2.48
Solvent content (%): 50.31
Ligand: 4-[(5-phenyl-1~{H}-imidazol-2-yl)methylamino]-2-(pyridin-3-ylmethoxy)benzenecarboximidamide (J08)
Ligand formula: C23 H22 N6 O
Ligand molecular weight: 398.46
Ligand SMILES: c1ccc(cc1)c2cnc([nH]2)CNc3ccc(c(c3)OCc4cccnc4)C(=N)N
Ligand InChI: InChI=1S/C23H22N6O/c24-23(25)19-9-8-18(11-21(19)30-15-16-5-4-10-26-12-16)27-14-22-28-13-20(29-22)17-6-2-1-3-7-17/h1-13,27H,14-15H2,(H3,24,25)(H,28,29)
Release date: 2019-05-08
Crystal Structure of Human Hexokinase 2 with cmpd 1, a C-2-substituted glucosamine (PDB entry 5HG1)
Macromolecule: Hexokinase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.1
Sequence length: 922 residues
Sequence: MGSSHHHHHHSSGLENLYFQGSDQVQKVDQYLYHMRLSDETLLEISKRFRKEMEKGLGATTHPTAAVKMLPTFVRSTPDGTEHGEFLALDLGGTNFRVLWVKVTDNGLQKVEMENQIYAIPEDIMRGSGTQLFDHIAECLANFMDKLQIKDKKLPLGFTFSFPCHQTKLDESFLVSWTKGFKSSGVEGRDVVALIRKAIQRRGDFDIDIVAVVNDTVGTMMTCGYDDHNCEIGLIVGTGSNACYMEEMRHIDMVEGDEGRMCINMEWGAFGDDGSLNDIRTEFDQEIDMGSLNPGKQLFEKMISGMYMGELVRLILVKMAKEELLFGGKLSPELLNTGRFETKDISDIEGEKDGIRKAREVLMRLGLDPTQEDCVATHRICQIVSTRSASLCAATLAAVLQRIKENKGEERLRSTIGVDGSVYKKHPHFAKRLHKTVRRLVPGCDVRFLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEHLQLSHDQLLEVKRRMKVEMERGLSKETHASAPVKMLPTYVCATPDGTEKGDFLALDLGGTNFRVLLVRVRNGKWGGVEMHNKIYAIPQEVMHGTGDELFDHIVQCIADFLEYMGMKGVSLPLGFTFSFPCQQNSLDESILLKWTKGFKASGCEGEDVVTLLKEAIHRREEFDLDVVAVVNDTVGTMMTCGFEDPHCEVGLIVGTGSNACYMEEMRNVELVEGEEGRMCVNMEWGAFGDNGCLDDFRTEFDVAVDELSLNPGKQRFEKMISGMYLGEIVRNILIDFTKRGLLFRGRISERLKTRGIFETKFLSQIESDCLALLQVRAILQHLGLESTCDDSIIVKEVCTVVARRAAQLCGAGMAAVVDRIRENRGLDALKVTVGVDGTLYKLHPHFAKVMHETVKDLAPKCDVSFLQSEDGSGKGAALITAVACRIREAGQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.76
R work: 0.2177
R free: 0.2658
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 296
Crystal growth procedure: protein: 6.6 mgs/mL, 10mM Tris HCL, pH=8, 0.1 M NaCl, 1mM DTT, 20mM MgCl2
Well: 0.2 M Na Citrate pH 5.5, 14-24 % PEG3350, 20 % ethylene glycol
Matthews coefficient: 4.83
Solvent content (%): 74.56
Ligand: 2-deoxy-2-{[(2E)-3-(3,4-dichlorophenyl)prop-2-enoyl]amino}-alpha-D-glucopyranose (62C)
Ligand formula: C15 H17 Cl2 N O6
Ligand molecular weight: 378.205
Ligand SMILES: c1cc(c(cc1C=CC(=O)NC2C(C(C(OC2O)CO)O)O)Cl)Cl
Ligand InChI: InChI=1S/C15H17Cl2NO6/c16-8-3-1-7(5-9(8)17)2-4-11(20)18-12-14(22)13(21)10(6-19)24-15(12)23/h1-5,10,12-15,19,21-23H,6H2,(H,18,20)/b4-2+/t10-,12-,13-,14-,15+/m1/s1
Release date: 2016-03-30
Human Tankyrase-2 in Complex with Macrocyclised Extended Peptide cp4n4m5 (PDB entry 5BXU)
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): 1.35
R work: 0.15619
R free: 0.18634
Average B factor: 15.263
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 1.60 M tri-sodium citrate
Matthews coefficient: 1.91
Solvent content (%): 35.63
Ligand: 4,4'-pentane-1,5-diylbis(1-propyl-1H-1,2,3-triazole) (4XQ)
Ligand formula: C15 H26 N6
Ligand molecular weight: 290.407
Ligand SMILES: CCCn1cc(nn1)CCCCCc2cn(nn2)CCC
Ligand InChI: InChI=1S/C15H26N6/c1-3-10-20-12-14(16-18-20)8-6-5-7-9-15-13-21(11-4-2)19-17-15/h12-13H,3-11H2,1-2H3
Release date: 2016-06-29
Crystal structure of human MGME1 with single strand DNA2 and Ca2+ (PDB entry 5ZYV)
Macromolecule: Mitochondrial genome maintenance exonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 254 residues
Sequence: GEDRRVPQNWFPIFNPERSDKPNASDPSVPLKIPLQRNVIPSVTRVLQQTMTKQQVFLLERWKQRMILELGEDGFKEYTSNVFLQGKRFQEALESILSPQETLKERDENLLKSGYIESVQHILKDVSGVRALESAVQHETLNYIGLLDCVAEYQGKLCVIDWKTSEKPKPFIQSTFDNPLQVVAYMGAMNHDTNYSFQVQCGLIVVAYKDGSPAHPHFMDAELCSQYWTKWLLRLEEYTEKKKNQNIQKPEYSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.72
R work: 0.2116
R free: 0.2539
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1M CHESpH 9.5 and 20% PEG 8000
Matthews coefficient: 2.11
Solvent content (%): 41.72
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: 2018-09-19
Crystal structure MMP-9 complexes with a constrained hydroxamate based inhibitor LT4 (PDB entry 5CUH)
Macromolecule: Matrix metalloproteinase-9,Matrix metalloproteinase-9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.35
Sequence length: 164 residues
Sequence: GFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.17253
R free: 0.21368
Average B factor: 18.239
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.25
Crystallization temperature (K): 293
Crystal growth procedure: 40% MPEG 5K, pH 7.25, 18% MPEG 2K
Matthews coefficient: 2.2
Solvent content (%): 44.03
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: 2016-02-10
Crystal Structure of human GGT1 in complex with Glutamate (with all atoms of glutamate) (PDB entry 4ZCG)
Macromolecule: Gamma-glutamyltranspeptidase 1 heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.2
Sequence length: 353 residues
Sequence: SASKEPDNHVYTRAAVAADAKQCSKIGRDALRDGGSAVDAAIAALLCVGLMNAHSMGIGGGLFLTIYNSTTRKAEVINAREVAPRLAFATMFNSSEQSQKGGLSVAVPGEIRGYELAHQRHGRLPWARLFQPSIQLARQGFPVGKGLAAALENKRTVIEQQPVLCEVFCRDRKVLREGERLTLPQLADTYETLAIEGAQAFYNGSLTAQIVKDIQAAGGIVTAEDLNNYRAELIEHPLNISLGDAVLYMPSAPLSGPVLALILNILKGYNFSRESVESPEQKGLTYHRIVEAFRFAYAKRTLLGDPKFVDVTEVVRNMTSEFFAAQLRAQISDDTTHPISYYKPEFYTPDDGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.1463
R free: 0.1852
Average B factor: 35.053
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: PEG3350, NH4Cl
Matthews coefficient: 2.93
Solvent content (%): 57.99
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-06-03
Structure of the EphA2 CRD bound to FabS1CE_C1, trigonal form (PDB entry 8TRS)
Macromolecule: S1CE variant of Fab C1 heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 222 residues
Sequence: EVQLVESGGGLVQPGGSLRLSCAASGFTIYYSSMHWVRQAPGKGLEWVASISSYYGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARYYAMDYWGQGTLVTVFNQIKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.18
R free: 0.214
Average B factor: 50.17
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 200 mM ammonium chloride, 30% PEG600 (GRAS1 condition A8)
Matthews coefficient: 2.82
Solvent content (%): 56.39
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: 2023-11-22
Crystal Structure of CK2alpha with 3,4-dichlorophenethylamine bound (PDB entry 5CLP)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.684
R work: 0.1778
R free: 0.1933
Average B factor: 31.89
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 107mM Mes pH 6.5, 29% glycerol ethoxylate, 1 M ammonium acetate
Matthews coefficient: 2.26
Solvent content (%): 45.63
Ligand: 2-(3,4-dichlorophenyl)ethanamine (42J)
Ligand formula: C8 H9 Cl2 N
Ligand molecular weight: 190.07
Ligand SMILES: c1cc(c(cc1CCN)Cl)Cl
Ligand InChI: InChI=1S/C8H9Cl2N/c9-7-2-1-6(3-4-11)5-8(7)10/h1-2,5H,3-4,11H2
Release date: 2016-07-27
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1255459547 (PDB entry 7G8M)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.029
R work: 0.2094
R free: 0.2598
Average B factor: 51.46
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.49
Solvent content (%): 50.69
Ligand: N-(1H-indol-7-yl)acetamide (Z0I)
Ligand formula: C10 H10 N2 O
Ligand molecular weight: 174.199
Ligand SMILES: CC(=O)Nc1cccc2c1[nH]cc2
Ligand InChI: InChI=1S/C10H10N2O/c1-7(13)12-9-4-2-3-8-5-6-11-10(8)9/h2-6,11H,1H3,(H,12,13)
Release date: 2023-07-12
JAK2 JH2 in complex with NVP-BSK805 (PDB entry 5UT4)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLIREEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1786
R free: 0.2198
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris, pH 8.0
0.2M Sodium acetate
12-20% PEG 4,000
Matthews coefficient: 2.23
Solvent content (%): 44.84
Ligand: 8-[3,5-difluoro-4-(morpholin-4-ylmethyl)phenyl]-2-(1-piperidin-4-yl-1H-pyrazol-4-yl)quinoxaline (DQX)
Ligand formula: C27 H28 F2 N6 O
Ligand molecular weight: 490.548
Ligand SMILES: c1cc(c2c(c1)ncc(n2)c3cnn(c3)C4CCNCC4)c5cc(c(c(c5)F)CN6CCOCC6)F
Ligand InChI: InChI=1S/C27H28F2N6O/c28-23-12-18(13-24(29)22(23)17-34-8-10-36-11-9-34)21-2-1-3-25-27(21)33-26(15-31-25)19-14-32-35(16-19)20-4-6-30-7-5-20/h1-3,12-16,20,30H,4-11,17H2
Release date: 2017-06-07
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMSOA001440b (PDB entry 7GSX)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.1976
R free: 0.2225
Average B factor: 35.202
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.31
Solvent content (%): 62.8
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: 2024-01-24
The Fk1 domain of FKBP51 in complex with (S)-(R)-3-(3,4-dimethoxyphenyl)-1-(3-(2-morpholinoethoxy)phenyl)propyl 1-((1R,4aR,8aR)-4-oxodecahydronaphthalene-1-carbonyl)piperidine-2-carboxylate (PDB entry 6SAF)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1903
R free: 0.2731
Average B factor: 48.131
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 28 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5
Matthews coefficient: 2.4
Solvent content (%): 48.68
Ligand: [(1~{R})-3-(3,4-dimethoxyphenyl)-1-[3-(2-morpholin-4-ylethoxy)phenyl]propyl] (2~{S})-1-[[(1~{R},4~{a}~{R},8~{a}~{R})-4-oxidanylidene-2,3,4~{a},5,6,7,8,8~{a}-octahydro-1~{H}-naphthalen-1-yl]carbonyl]piperidine-2-carboxylate (L2Q)
Ligand formula: C40 H54 N2 O8
Ligand molecular weight: 690.865
Ligand SMILES: COc1ccc(cc1OC)CCC(c2cccc(c2)OCCN3CCOCC3)OC(=O)C4CCCCN4C(=O)C5CCC(=O)C6C5CCCC6
Ligand InChI: InChI=1S/C40H54N2O8/c1-46-37-18-14-28(26-38(37)47-2)13-17-36(29-8-7-9-30(27-29)49-25-22-41-20-23-48-24-21-41)50-40(45)34-12-5-6-19-42(34)39(44)33-15-16-35(43)32-11-4-3-10-31(32)33/h7-9,14,18,26-27,31-34,36H,3-6,10-13,15-17,19-25H2,1-2H3/t31-,32-,33-,34+,36-/m1/s1
Release date: 2019-12-18
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z2895259681 (PDB entry 5QP5)
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): 1.9
R work: 0.202
R free: 0.2526
Average B factor: 58.509
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: 2.52
Solvent content (%): 51.1
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2019-05-08
Structure of CDK2 in complex with FP19711, a Helicon Polypeptide (PDB entry 7UXI)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 299 residues
Sequence: GMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.2101
R free: 0.2636
Average B factor: 40.5748
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M Tris pH 8.5, 25% w/v PEG 2,000MME
Matthews coefficient: 1.8
Solvent content (%): 31.67
Ligand: AMINO GROUP (NH2)
Ligand formula: H2 N
Ligand molecular weight: 16.023
Ligand SMILES: [NH2]
Ligand InChI: InChI=1S/H3N/h1H3
Release date: 2022-12-28
Structure of HDAC2 in complex with an inhibitor (compound 19) (PDB entry 7MOY)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1782
R free: 0.2083
Average B factor: 29.35
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.48
Solvent content (%): 50.37
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: 2021-07-14
Rapid Discovery of Pyrido[3,4-d]pyrimidine Inhibitors of Monopolar Spindle kinase 1 (MPS1) Using a Structure-Based Hydridization Approach (PDB entry 5EI8)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.2141
R free: 0.2441
Average B factor: 64.52
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M BIS-TRIS Propane
0.2 M NgCl2
0.2 M Sodium formate
20 % PEG3350
Matthews coefficient: 2.77
Solvent content (%): 55.1
Ligand: ~{N}-[2-methoxy-4-(1-methylpyrazol-4-yl)phenyl]-8-(1-methylpyrazol-4-yl)pyrido[3,4-d]pyrimidin-2-amine (5OE)
Ligand formula: C22 H20 N8 O
Ligand molecular weight: 412.447
Ligand SMILES: Cn1cc(cn1)c2ccc(c(c2)OC)Nc3ncc4ccnc(c4n3)c5cnn(c5)C
Ligand InChI: InChI=1S/C22H20N8O/c1-29-12-16(10-25-29)14-4-5-18(19(8-14)31-3)27-22-24-9-15-6-7-23-20(21(15)28-22)17-11-26-30(2)13-17/h4-13H,1-3H3,(H,24,27,28)
Release date: 2016-04-20
USP28 USP domain apo (PDB entry 8P19)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 28
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 377 residues
Sequence: GPNPNDWRRVDGWPVGLKNVGNTCWFSAVIQSLFQLPEFRRLVLSYSLPQNVLENCRSHTEKRNIMFMQELQYLFALMMGSNRKFVDPSAALDLLKGAFRSSEEQQQDVSEFTHKLLDWLEDAFQLAVNVNSPRNKSENPMVQLFYGTFLTEGVREGKPFCNNETFGQYPLQVNGYRNLDECLEGAMVEGDVELLPSDHSVKYGQERWFTKLPPVLTFELSRFEFNQSLGQPEKIHNKLEFPQIIYMDRYMYGSGSGSRQVPYRLHAVLVHEGQANAGHYWAYIYNQPRQSWLKYNDISVTESSWEEVERDSYGGLRNVSAYCLMYINDKLPYFNAEAAPTESDQMSEVEALSVELKHYIQEDNWRFEQEVEEWEEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.1939
R free: 0.2217
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.05M NaCl
0.1M Li2SO4
0.1M MES pH 6.4
14% PEG4000
Matthews coefficient: 4.1
Solvent content (%): 69.99
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: 2024-05-22
Crystal structure of TTBK1 in complex with compound 9 (7-005) (PDB entry 7ZHP)
Macromolecule: Tau-tubulin kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 309 residues
Sequence: MNMSGGGEQADILPANYVVKDRWKVLKKIGGGGFGEIYEAMDLLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNEKFNYVVMQLQGRNLADLRRSQPRGTFTLSTTLRLGKQILESIEAIHSVGFLHRDIKPSNFAMGRLPSTYRKCYMLDFGLARQYTNTTGDVRPPRNVAGFRGTVRYASVNAHKNREMGRHDDLWSLFYMLVEFAVGQLPWRKIKDKEQVGMIKEKYEHRMLLKHMPSEFHLFLDHIASLDYFTKPDYQLIMSVFENSMKERGIAENEAFDWEKAGTDALLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1765
R free: 0.218
Average B factor: 31.494
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 14-23% PEG 3350, 0.2 M sodium acetate pH 7.0 and 0.1 M tris pH 7.5-9.0
Matthews coefficient: 2.34
Solvent content (%): 47.42
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2023-04-19
Structural basis of tubulin detyrosination (PDB entry 6JZC)
Macromolecule: Tubulinyl-Tyr carboxypeptidase 2
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 3.4.17.17
Sequence length: 355 residues
Sequence: MTGSAADTHRCPHPKITKGTRSRSSHARPVSLATSGGSEEEDKDGGVLFHVNKSGFPIDSHTWERMWLHVAKVHPRGGEMVGAIRNAAFLAKPSIPQVPNYRLSMTIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKCLEAVILGIYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGYYGSLGMSRRAELMDKPLTFRTLSDLVFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEKYARDMRMKILKPASAHSPTQVRSRGKSLSPRRRQASPPRRLGRRDKSPALTEKKVADLGTLNEVGYQIRI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.201
R work: 0.1809
R free: 0.2148
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 291.15
Crystal growth procedure: HEPES, Ammonium sulphate, potassium chloride
Matthews coefficient: 2.35
Solvent content (%): 47.57
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: 2019-07-17