satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of PIM1 with inhibitor: 5-(3,4-dichlorophenyl)-1~{H}-pyrazol-3-amine (PDB entry 5KGE)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 276 residues
Sequence: EKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.196
R free: 0.208
Average B factor: 53.58
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG 3350, 0.2 M Na2SO4, 6% ethylene glycol, 0.1 M Tris, pH 7.3
Matthews coefficient: 3.43
Solvent content (%): 64.13
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: 2017-08-09
Crystal structure of Drosophila Poglut1 (Rumi) complexed with its substrate protein (EGF repeat) (PDB entry 5F86)
Macromolecule: O-glucosyltransferase rumi
Type: Protein, polypeptide(L)
Source organism: Drosophila melanogaster
EC number: 2.4.1
Sequence length: 402 residues
Sequence: AAQPAEALEDDGLCSADQKSCAQSEPDQINEDEFSFKIRRQIEKANADYKPCSSDPQDSDCSCHANVLKRDLAPYKSTGVTRQMIESSARYGTKYKIYGHRLYRDANCMFPARCEGIEHFLLPLVATLPDMDLIINTRDYPQLNAAWGNAAGGPVFSFSKTKEYRDIMYPAWTFWAGGPATKLHPRGIGRWDQMREKLEKRAAAIPWSQKRSLGFFRGSRTSDERDSLILLSRRNPELVEAQYTKNQGWKSPKDTLDAPAADEVSFEDHCKYKYLFNFRGVAASFRLKHLFLCKSLVFHVGDEWQEFFYDQLKPWVHYVPLKSYPSQQEYEHILSFFKKNDALAQEIAQRGYDFIWEHLRMKDIKCYWRKLLKRYVKLLQYEVKPEDQLIYIGPKARALVPR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.19553
R free: 0.2212
Average B factor: 25.723
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.62M ammonium sulfate
Matthews coefficient: 3.17
Solvent content (%): 61.22
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: 2016-07-20
Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate SuBKA (PDB entry 5XHS)
Macromolecule: NAD-dependent protein deacylase sirtuin-5, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1
Sequence length: 288 residues
Sequence: MGHHHHHHSGENLYFQGASARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.19
R work: 0.1731
R free: 0.2243
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 23% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.2M NaCl
Matthews coefficient: 2.3
Solvent content (%): 46.42
Ligand: benzyl chlorocarbonate (PHQ)
Ligand formula: C8 H7 Cl O2
Ligand molecular weight: 170.593
Ligand SMILES: c1ccc(cc1)COC(=O)Cl
Ligand InChI: InChI=1S/C8H7ClO2/c9-8(10)11-6-7-4-2-1-3-5-7/h1-5H,6H2
Release date: 2018-05-02
Human ppGalNAcT2 I253A/L310A Mutant with EA2 and UDP (PDB entry 6E7I)
Macromolecule: Polypeptide N-acetylgalactosaminyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.41
Sequence length: 535 residues
Sequence: MGILPSPGMPALLSLVSLLSVLLMGCVAETGKVRWPDFNQEAYVGGTMVRSGQDPYARNKFNQVESDKLRMDRAIPDTRHDQCQRKQWRVDLPATSVVITFHNEARSALLRTVVSVLKKSPPHLIKEIILVDDYSNDPEDGALLGKIEKVRVLRNDRREGLMRSRVRGADAAQAKVLTFLDSHCECNEHWLEPLLERVAEDRTRVVSPIADVINMDNFQYVGASADLKGGFDWNLVFKWDYMTPEQRRSRQGNPVAPIKTPMIAGGAFVMDKFYFEELGKYDMMMDVWGGENLEISFRVWQCGGSLEIIPCSRVGHVFRKQHPYTFPGGSGTVFARNTRRAAEVWMDEYKNFYYAAVPSARNVPYGNIQSRLELRKKLSCKPFKWYLENVYPELRVPDHQDIAFGALQQGTNCLDTLGHFADGVVGVYECHNAGGNQEWALTKEKSVKHMDLCLTVVDRAPGSLIKLQGCRENDSRQKWEQIEGNSKLRHVGSNLCLDSRTAKSGGLSVEVCGPALSQQWKFTLNLQQKHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16719
R free: 0.2155
Average B factor: 16.453
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG8000, HEPES
Matthews coefficient: 1.9
Solvent content (%): 35.23
Ligand: URIDINE-5'-DIPHOSPHATE (UDP)
Ligand formula: C9 H14 N2 O12 P2
Ligand molecular weight: 404.161
Ligand SMILES: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
Release date: 2020-01-29
Structure of TAK1 in complex with compound 22 (PDB entry 7NTI)
Macromolecule: Mitogen-activated protein kinase 7,TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 315 residues
Sequence: GSLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.2205
R free: 0.2491
Average B factor: 61.914
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.9
Crystallization temperature (K): 293
Crystal growth procedure: 0.60 M Sodium Chloride, 0.60 M Sodium Citrate, 0.10 M Tris-HCl pH 7.9
Matthews coefficient: 4.03
Solvent content (%): 69.48
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: 2021-04-07
Human Ubc9 with covalent isopeptide ligand (PDB entry 6SYF)
Macromolecule: ACE-LEU-ARG-LEU-ARG-GLY-CYS
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 7 residues
Sequence: XLRLRGC
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2129
R free: 0.263
Average B factor: 30.76
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M trisodium citrate pH 5.0, 30% PEG8000
Matthews coefficient: 2.06
Solvent content (%): 40.3
Release date: 2020-08-12
Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (P199A) (PDB entry 5D1M)
Macromolecule: Ubiquitin-conjugating enzyme E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2.19
Sequence length: 147 residues
Sequence: MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.581
R work: 0.1882
R free: 0.2231
Average B factor: 27.7522
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 20% PEG 10000, 8% Ethylene glycol, 0.1M HEPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Matthews coefficient: 2.32
Solvent content (%): 46.96
Ligand: OXALATE ION (OXL)
Ligand formula: C2 O4
Ligand molecular weight: 88.019
Ligand SMILES: C(=O)(C(=O)[O-])[O-]
Ligand InChI: InChI=1S/C2H2O4/c3-1(4)2(5)6/h(H,3,4)(H,5,6)/p-2
Release date: 2015-10-28
Structure of Compound 17 bound to CK2alpha (PDB entry 8AEC)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 328 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.09
R work: 0.195
R free: 0.2086
Average B factor: 17.11
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.03
Solvent content (%): 39.34
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2022-10-12
Crystal structure of human Cathepsin-S with bound ligand (PDB entry 5QC6)
Macromolecule: Cathepsin S
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.27
Sequence length: 223 residues
Sequence: ILPDSVDWREKGCVTEVKYQGSCGASWAFSAVGALEAQLKLKTGKLVSLSAQNLVDCSTEKYGNKGCNGGFMTTAFQYIIDNKGIDSDASYPYKAMDQKCQYDSKYRAATCSKYTELPYGREDVLKEAVANKGPVSVGVDARHPSFFLYRSGVYYEPSCTQNVNHGVLVVGYGDLNGKEYWLVKNSWGHNFGEEGYIRMARNKGNHCGIASFPSYPEILQGGG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.144
R free: 0.181
Average B factor: 16.6
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 293
Crystal growth procedure: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K
Matthews coefficient: 2.25
Solvent content (%): 45.35
Ligand: (4~{S})-1-[1-[(2~{S})-3-[3-[3-[2-(4-methylpiperidin-1-yl)ethylsulfanyl]-4-(trifluoromethyl)phenyl]-5-methylsulfonyl-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-1-yl]-2-oxidanyl-propyl]piperidin-4-yl]-4-oxidanyl-pyrrolidin-2-one (BCJ)
Ligand formula: C34 H49 F3 N6 O5 S2
Ligand molecular weight: 742.915
Ligand SMILES: CC1CCN(CC1)CCSc2cc(ccc2C(F)(F)F)c3c4c(n(n3)CC(CN5CCC(CC5)N6CC(CC6=O)O)O)CCN(C4)S(=O)(=O)C
Ligand InChI: InChI=1S/C34H49F3N6O5S2/c1-23-5-10-39(11-6-23)15-16-49-31-17-24(3-4-29(31)34(35,36)37)33-28-22-41(50(2,47)48)14-9-30(28)43(38-33)21-27(45)19-40-12-7-25(8-13-40)42-20-26(44)18-32(42)46/h3-4,17,23,25-27,44-45H,5-16,18-22H2,1-2H3/t26-,27-/m0/s1
Release date: 2017-12-20
Structure of human DPP3 in complex with met-enkephalin (PDB entry 5E33)
Macromolecule: Dipeptidyl peptidase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.14.4
Sequence length: 726 residues
Sequence: MADTQYILPNDIGVSSLDSREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMEDAKLAQDFLDSQNLSAYNTRLFKEVDGCGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFRGSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWPPTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQREKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPETGEQIQSWYRCGETWDSKFSTIASSYEECRAESVGLYLSLHPQVLEIFGFEGADAEDVIYVNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPDARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPESFLTLRDTVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLATADARFW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.837
R work: 0.1815
R free: 0.2237
Average B factor: 37
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phospahte dibasic,
pH- 8.2
Matthews coefficient: 2.51
Solvent content (%): 51.04
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: 2016-04-13
BRAF-MEK complex with AMP-PCP bound to BRAF (PDB entry 6U2G)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 394 residues
Sequence: GSPKKKPTPIQLNPAPDGSAVNGTSSAETNLEALQKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGCQVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.886
R work: 0.229
R free: 0.2757
Average B factor: 79.0371
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: Ammonium sulfate, MES, PEK 8000
Matthews coefficient: 3.29
Solvent content (%): 62.65
Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER (ACP)
Ligand formula: C11 H18 N5 O12 P3
Ligand molecular weight: 505.208
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
Release date: 2019-08-28
DNA Ligase 1 with nick DNA 3'rG:C (PDB entry 8VDS)
Macromolecule: DNA ligase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.5.1.1
Sequence length: 658 residues
Sequence: LDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGEDSGSDPEDT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.196
R free: 0.252
Average B factor: 90.32
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 298.15
Crystal growth procedure: 100 mM MES, pH 6.4, 100 mM Lithium acetate, 12% PEG3350
Matthews coefficient: 2.78
Solvent content (%): 55.8
Release date: 2024-05-22
Crystal Structure of human cyclic GMP-AMP synthase in complex with 2-[(4-phenylphenyl)methylamino]-5-(trifluoromethyl)-4H-[1,2,4]triazolo[1,5-a]pyrimidin-7-one (PDB entry 7FU0)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.969
R work: 0.2156
R free: 0.2801
Average B factor: 57.5598
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Matthews coefficient: 2.47
Solvent content (%): 50.1
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2024-02-21
MET Tyrosine Kinase Inhibition Enhances the Antitumor Efficacy of an HGF Antibody (PDB entry 5UAD)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 343 residues
Sequence: GAMGSQVQYPLTDMSPILTSGDSDISSPLLQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHYVHVNATYVNVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1961
R free: 0.2517
Average B factor: 49.075
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 273
Crystal growth procedure: 19.% PEG 3350, 12.% Isopropanol, 0.1M HEPES pH 7.2
Matthews coefficient: 2.11
Solvent content (%): 44.77
Ligand: N-(6-{[6-(1-methyl-1H-pyrazol-4-yl)-1H-benzotriazol-1-yl]methyl}imidazo[1,2-b]pyridazin-2-yl)cyclopropanecarboxamide (84P)
Ligand formula: C21 H19 N9 O
Ligand molecular weight: 413.435
Ligand SMILES: Cn1cc(cn1)c2ccc3c(c2)n(nn3)Cc4ccc5nc(cn5n4)NC(=O)C6CC6
Ligand InChI: InChI=1S/C21H19N9O/c1-28-10-15(9-22-28)14-4-6-17-18(8-14)29(27-25-17)11-16-5-7-20-23-19(12-30(20)26-16)24-21(31)13-2-3-13/h4-10,12-13H,2-3,11H2,1H3,(H,24,31)
Release date: 2017-05-31
Crystal structure of ligase I with nick duplexes containing mismatch A:C (PDB entry 7SX5)
Macromolecule: DNA ligase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.5.1.1
Sequence length: 669 residues
Sequence: LDPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGEDSGSDPEDTAAALEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1752
R free: 0.2119
Average B factor: 38.3039
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES pH 6.6, 100 mM lithium acetate, 20% (w/v) polyethylene glycol PEG3350
Matthews coefficient: 2.6
Solvent content (%): 52.68
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: 2022-07-13
Crystal structure of EloBC-VHL-CDO1 complex bound to compound 4 molecular glue (PDB entry 8VLB)
Macromolecule: von Hippel-Lindau disease tumor suppressor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 162 residues
Sequence: GPMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.208
R free: 0.2581
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.2M SODIUM CITRATE, 0.1M BIS-TRIS-PROPANE PH 6.5, 20% PEG3350
Matthews coefficient: 4.11
Solvent content (%): 70.05
Ligand: N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide (3JF)
Ligand formula: C24 H32 N4 O4 S
Ligand molecular weight: 472.6
Ligand SMILES: Cc1c(scn1)c2ccc(cc2)CNC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)C)O
Ligand InChI: InChI=1S/C24H32N4O4S/c1-14-20(33-13-26-14)17-8-6-16(7-9-17)11-25-22(31)19-10-18(30)12-28(19)23(32)21(24(3,4)5)27-15(2)29/h6-9,13,18-19,21,30H,10-12H2,1-5H3,(H,25,31)(H,27,29)/t18-,19+,21-/m1/s1
Release date: 2024-03-13
Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a) (PDB entry 6YHG)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.1233
R free: 0.1451
Average B factor: 17.8975
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20mM sodium dihydrogen phosphate ph 7.5
350mM NaCl
27% PEG 8000
Matthews coefficient: 2.4
Solvent content (%): 49.21
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: 2021-04-07
Crystal Structure of PDE2 in complex with compound 16 (PDB entry 6B96)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 373 residues
Sequence: MHHHHHHENLYFQGELSTSLYKKAGFDDDDKSDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1754
R free: 0.2067
Average B factor: 33.39
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Hepes pH7.5, 12% PEG8000
Matthews coefficient: 2.05
Solvent content (%): 39.95
Ligand: 6-chloro-N-{1-[4-(trifluoromethyl)phenyl]cyclopropyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine (CZV)
Ligand formula: C15 H11 Cl F3 N5
Ligand molecular weight: 353.73
Ligand SMILES: c1cc(ccc1C2(CC2)Nc3c4cn[nH]c4nc(n3)Cl)C(F)(F)F
Ligand InChI: InChI=1S/C15H11ClF3N5/c16-13-21-11(10-7-20-24-12(10)22-13)23-14(5-6-14)8-1-3-9(4-2-8)15(17,18)19/h1-4,7H,5-6H2,(H2,20,21,22,23,24)
Release date: 2017-11-22