satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with cyclosulfamidate 4 (PDB entry 7P2Z)
Macromolecule: Lysosomal alpha-glucosidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.20
Sequence length: 872 residues
Sequence: QCDVPPNSRFDCAPDKAITQEQCEARGCCYIPAKQGLQGAQMGQPWCFFPPSYPSYKLENLSSSEMGYTATLTRTTPTFFPKDILTLRLDVMMETENRLHFTIKDPANRRYEVPLETPRVHSRAPSPLYSVEFSEEPFGVIVHRQLDGRVLLNTTVAPLFFADQFLQLSTSLPSQYITGLAEHLSPLMLSTSWTRITLWNRDLAPTPGANLYGSHPFYLALEDGGSAHGVFLLNSNAMDVVLQPSPALSWRSTGGILDVYIFLGPEPKSVVQQYLDVVGYPFMPPYWGLGFHLCRWGYSSTAITRQVVENMTRAHFPLDVQWNDLDYMDSRRDFTFNKDGFRDFPAMVQELHQGGRRYMMIVDPAISSSGPAGSYRPYDEGLRRGVFITNETGQPLIGKVWPGSTAFPDFTNPTALAWWEDMVAEFHDQVPFDGMWIDMNEPSNFIRGSEDGCPNNELENPPYVPGVVGGTLQAATICASSHQFLSTHYNLHNLYGLTEAIASHRALVKARGTRPFVISRSTFAGHGRYAGHWTGDVWSSWEQLASSVPEILQFNLLGVPLVGADVCGFLGNTSEELCVRWTQLGAFYPFMRNHNSLLSLPQEPYSFSEPAQQAMRKALTLRYALLPHLYTLFHQAHVAGETVARPLFLEFPKDSSTWTVDHQLLWGEALLITPVLQAGKAEVTGYFPLGTWYDLQTVPIEALGSLPPPPAAPREPAIHSEGQWVTLPAPLDTINVHLRAGYIIPLQGPGLTTTESRQQPMALAVALTKGGEARGELFWDDGESLEVLERGAYTQVIFLARNNTIVNELVRVTSEGAGLQLQKVTVLGVATAPQQVLSNGVPVSNFTYSPDTKVLDICVSLLMGEQFLVSWC
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1485
R free: 0.1753
Average B factor: 28.703
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 1.9 M AMMONIUM SULPHATE, 0.1 M HEPES     
REMARK 280  PH 7.0, 2% V/V PEG400
Matthews coefficient: 3.4
Solvent content (%): 63
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: 2022-07-13
Crystal structure of IRAK4 in complex with compound 30 (PDB entry 5UIU)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 323 residues
Sequence: MHHHHHHGGENLYFQGENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.1854
R free: 0.2044
Average B factor: 46.34
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 1.6-1.8M Ammonium Citrate, pH7.0
Matthews coefficient: 2.53
Solvent content (%): 51.33
Ligand: 1-{[(2S,3S,4S)-3-ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (8CG)
Ligand formula: C18 H20 F N3 O4
Ligand molecular weight: 361.368
Ligand SMILES: CCC1C(NC(=O)C1F)COc2c3cc(c(cc3ccn2)C(=O)N)OC
Ligand InChI: InChI=1S/C18H20FN3O4/c1-3-10-13(22-17(24)15(10)19)8-26-18-11-7-14(25-2)12(16(20)23)6-9(11)4-5-21-18/h4-7,10,13,15H,3,8H2,1-2H3,(H2,20,23)(H,22,24)/t10-,13+,15-/m0/s1
Release date: 2017-05-24
Human cyclophilin A at 278K, Data set 8 (PDB entry 5KV6)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1692
R free: 0.2238
Average B factor: 21.6713
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
Matthews coefficient: 2.81
Solvent content (%): 56.3
Release date: 2016-08-10
C-terminal SANT-SLIDE domain of human Chromodomain-helicase-DNA-binding protein 4 (CHD4) (PDB entry 8D4Y)
Macromolecule: Chromodomain-helicase-DNA-binding protein 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 431 residues
Sequence: RSEAPRRPSRKGLRNDKDKPLPPLLARVGGNIEVLGFNARQRKAFLNAIMRYGMPPQDAFTTQWLVRDLRGKSEKEFKAYVSLFMRHLCEPGADGAETFADGVPREGLSRQHVLTRIGVMSLIRKKVQEFEHVNGRWSMPELAEVEENKKMSQPGSPSPKTPTPSTPGDTQPNTPAPVPPAEDGIKIEENSLKEEESIEGEKEVKSTAPETAIECTQAPAPASEDEKVVVEPPEGEEKVEKAEVKERTEEPMETEPKGAADVEKVEEKSAIDLTPIVVEDKEEKKEEEEKKEVMLQNGETPKDLNDEKQKKNIKQRFMFNIADGGFTELHSLWQNEERAATVTKKTYEIWHRRHDYWLLAGIINHGYARWQDIQNDPRYAILNEPFKGEMNRGNFLEIKNKFLARRFKLLEQALVIEEQLRRAAYLNMSED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2632
R free: 0.3012
Average B factor: 90.0746
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M bicine/Trizma base pH 8.3, 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M mixture of carboxylic acids*, and 20 mM spermidine 

*Sodium Formate; Ammonium 
acetate; Sodium citrate tribasic 
dihydrate; Potassium sodium tartrate 
tetrahydrate; Sodium oxamate
Matthews coefficient: 2.16
Solvent content (%): 43.08
Release date: 2022-12-21
Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives (PDB entry 5LSU)
Macromolecule: Histone-lysine N-methyltransferase NSD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 252 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMKLLRELRETQESERKPPPYKHIKVNKPYGKVQIYTADISEIPKCNCKPTDENPCGFDSECLNRMLMFECHPQVCPAGEFCQNQCFTKRQYPETKIIKTLQRGWGLVAKRDIRKGEFVNEYVGELIDEEECMARIKHAHENDITHFYMLTIDKDRIIDAGPKGNYSRFMNHSCQPNCETLKWTVNGDTRVGLFAVCDIPAGTELTFNYNLDCLGNEKTVCRCGASNCSGFLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.171
R free: 0.238
Average B factor: 53.711
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16.0%w/v PEG 3350, 0.1M NH4Cl
Matthews coefficient: 2.1
Solvent content (%): 41.49
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: 2016-10-05
The crystal structure of CK2alpha in complex with an analogue of compound 22 (PDB entry 5OTS)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 342 residues
Sequence: SGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVAAAKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2029
R free: 0.2449
Average B factor: 29.65
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 1.99
Solvent content (%): 38.33
Ligand: 2-(1~{H}-benzimidazol-2-yl)ethyl-[[3,5-bis(chloranyl)-4-phenyl-phenyl]methyl]azanium (AU2)
Ligand formula: C22 H20 Cl2 N3
Ligand molecular weight: 397.32
Ligand SMILES: c1ccc(cc1)c2c(cc(cc2Cl)C[NH2+]CCc3[nH]c4ccccc4n3)Cl
Ligand InChI: InChI=1S/C22H19Cl2N3/c23-17-12-15(13-18(24)22(17)16-6-2-1-3-7-16)14-25-11-10-21-26-19-8-4-5-9-20(19)27-21/h1-9,12-13,25H,10-11,14H2,(H,26,27)/p+1
Release date: 2018-09-05
The X-RAY co-crystal structure of human FGFR3 V555M and Compound 17 (PDB entry 8UDV)
Macromolecule: Fibroblast growth factor receptor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 297 residues
Sequence: MSELELPADPKWELSRARLTLGKPLGEGCFGQVVMAEAIGIDKDRAAKPVTVAVKMLKDDATDKDLSDLVSEMEMMKMIGKHKNIINLLGACTQGGPLYVLMEYAAKGNLREFLRARRSGEEQLTFKDLVSCAYQVARGMEYLASQKCIHRDLAARNVLVTEDNVMKIADFGLARDVHNLDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLLWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTHDLYMIMRECWHAAPSQRPTFKQLVEDLDRVLTVTSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.348
R work: 0.2362
R free: 0.2612
Average B factor: 39.38
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.10 M BIS-TRIS/HCl pH 6.50,
0.20 M (NH4)2SO4,
25.00 % (w/v) PEG 3350
Matthews coefficient: 2.76
Solvent content (%): 55.49
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: 2024-02-07
DDR1, 3-[2-(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)phenyl]benzamide, 1.800A, P212121, Rfree=23.1% (PDB entry 5SAU)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1991
R free: 0.2312
Average B factor: 41.8181
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7.6 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed with reservoir consisting of 0.1M MES/NaOH pH 6.5, 0.2M KI, 25% PEG 4000
Matthews coefficient: 2.38
Solvent content (%): 48.42
Ligand: 3-[(6-aminopyridin-3-yl)ethynyl]-N-[3-(trifluoromethyl)phenyl]benzamide (1IF)
Ligand formula: C21 H14 F3 N3 O
Ligand molecular weight: 381.351
Ligand SMILES: c1cc(cc(c1)C(=O)Nc2cccc(c2)C(F)(F)F)C#Cc3ccc(nc3)N
Ligand InChI: InChI=1S/C21H14F3N3O/c22-21(23,24)17-5-2-6-18(12-17)27-20(28)16-4-1-3-14(11-16)7-8-15-9-10-19(25)26-13-15/h1-6,9-13H,(H2,25,26)(H,27,28)
Release date: 2022-06-29
Crystal structure of uPA in complex with S2444 (PDB entry 5WXS)
Macromolecule: Urokinase-type plasminogen activator chain B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.185
R free: 0.266
Average B factor: 56.81
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate, pH 4.6, 2.0M ammonium sulfate supplemented with 5% polyethylene glycol 400
Matthews coefficient: 2.12
Solvent content (%): 41.9
Ligand: (2R)-N-[2-[[(2S)-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-1,2-dihydropyrrole-2-carboxamide (7YF)
Ligand formula: C13 H20 N6 O4
Ligand molecular weight: 324.336
Ligand SMILES: C1=CC(=O)NC1C(=O)NCC(=O)NC(CCCNC(=N)N)C=O
Ligand InChI: InChI=1S/C13H20N6O4/c14-13(15)16-5-1-2-8(7-20)18-11(22)6-17-12(23)9-3-4-10(21)19-9/h3-4,7-9H,1-2,5-6H2,(H,17,23)(H,18,22)(H,19,21)(H4,14,15,16)/t8-,9+/m0/s1
Release date: 2018-07-11
Multiconformer model of apo WT PTP1B with glycerol at 278 K (PDB entry 6B8X)
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): 1.74
R work: 0.1752
R free: 0.2059
Average B factor: 31.4347
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 16% PEG 8000, 2% ethanol, 10% glycerol
Matthews coefficient: 3.54
Solvent content (%): 65.27
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: 2018-06-20
CDK2/cyclin A2 in complex with pyrazolo[4,3-d]pyrimidine inhibitor LGR4455 (PDB entry 6GVA)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 299 residues
Sequence: SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1943
R free: 0.2403
Average B factor: 39.552
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide, and 0.1 M bicine/Trizma base, pH 8.5
Matthews coefficient: 2.57
Solvent content (%): 52
Ligand: 5-(2-azanylethylsulfanyl)-3-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]-2~{H}-pyrazolo[4,3-d]pyrimidin-7-amine (FCQ)
Ligand formula: C22 H25 N7 S
Ligand molecular weight: 419.546
Ligand SMILES: CC(C)c1c2c(c(nc(n2)SCCN)NCc3ccc(cc3)c4ccccn4)n[nH]1
Ligand InChI: InChI=1S/C22H25N7S/c1-14(2)18-19-20(29-28-18)21(27-22(26-19)30-12-10-23)25-13-15-6-8-16(9-7-15)17-5-3-4-11-24-17/h3-9,11,14H,10,12-13,23H2,1-2H3,(H,28,29)(H,25,26,27)
Release date: 2019-05-01
Tricomplex of RMC-4998, KRAS G12C, and CypA (PDB entry 8G9P)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: SMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1563
R free: 0.1875
Average B factor: 20.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 22% PEG 3350, 100 mM NaCl
Matthews coefficient: 2.16
Solvent content (%): 43.06
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2023-08-16
Crystal structure of the catalytic domain of MMP-12 in complex with a selective sugar-conjugated arylsulfonamide carboxylate water-soluble inhibitor (DC27). (PDB entry 5I0L)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.175
R free: 0.253
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Protein-inhibitor complex:  hMMP12 0.631 milli-M + 0.010 M Acetohydroxamic acid + 0.005 M inhibitor DC27, 10% DMSO.
precipitant: 34% PEG 4K, 1.5 M imidazole piperidine, pH 8.5, Dioxane 25%
Cryoprotectant: 40% Cryomix: (12.5 % diethylene glycol + 12.5 % glycerol + 12.5 % 1,2-propanediol + 12.5 % 2,3-butanediol + 25 % DMSO + 30 % 1,4-dioxane), 25% MPEG 6K, 0.1 M AAB (Na acetate, ADA, Bicine: 10% acid/90% basic), pH 8.5
Matthews coefficient: 2.15
Solvent content (%): 42.82
Ligand: (2R)-2-[{(E)-2-[({(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-bis(acetyloxy)-6-[(acetyloxy)methyl]tetrahydro-2H-pyran-2-yl}carbamothioyl)amino]ethenyl}(biphenyl-4-ylsulfonyl)amino]-3-methylbutanoic acid (H27)
Ligand formula: C34 H42 N4 O12 S2
Ligand molecular weight: 762.847
Ligand SMILES: CC(C)C(C(=O)O)N(C=CNC(=S)NC1C(C(C(C(O1)COC(=O)C)OC(=O)C)OC(=O)C)NC(=O)C)S(=O)(=O)c2ccc(cc2)c3ccccc3
Ligand InChI: InChI=1S/C34H42N4O12S2/c1-19(2)29(33(43)44)38(52(45,46)26-14-12-25(13-15-26)24-10-8-7-9-11-24)17-16-35-34(51)37-32-28(36-20(3)39)31(49-23(6)42)30(48-22(5)41)27(50-32)18-47-21(4)40/h7-17,19,27-32H,18H2,1-6H3,(H,36,39)(H,43,44)(H2,35,37,51)/b17-16+/t27-,28-,29-,30-,31-,32-/m1/s1
Release date: 2016-07-06
A Novel UHRF1-Targeted Compound (PDB entry 8JIG)
Macromolecule: E3 ubiquitin-protein ligase UHRF1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 212 residues
Sequence: MPSNHYGPIPGIPVGTMWRFRVQVSESGVHRPHVAGIHGRSNDGAYSLVLAGGYEDDVDHGNFFTYTGSGGRDLSGNKRTAEQSCDQKLTNTNRALALNCFAPINDQEGAEAKDWRSGKPVRVVRNVKGGKNSKYAPAEGNRYDGIYKVVKYWPEKGKSGFLVWRYLLRRDDDEPGPWTKEGKDRIKKLGLTMQYPEGYLEALANAHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2076
R free: 0.2443
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bris-Tris, pH 6.0, 0.2M NaCl, 1mM TCEP, 2.2-2.4mM ammonium sulfate
Matthews coefficient: 2.52
Solvent content (%): 51.19
Ligand: N-[2,4-bis(oxidanylidene)-1H-pyrimidin-5-yl]-N'-oxidanyl-octanediamide (8JA)
Ligand formula: C12 H18 N4 O5
Ligand molecular weight: 298.295
Ligand SMILES: C1=C(C(=O)NC(=O)N1)NC(=O)CCCCCCC(=O)NO
Ligand InChI: InChI=1S/C12H18N4O5/c17-9(5-3-1-2-4-6-10(18)16-21)14-8-7-13-12(20)15-11(8)19/h7,21H,1-6H2,(H,14,17)(H,16,18)(H2,13,15,19,20)
Release date: 2024-05-29
Catalytic domain of human PARP-1 in complex with the inhibitor MC2050 (PDB entry 6XVW)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 354 residues
Sequence: HMSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKVEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKTSLW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2295
R free: 0.2647
Average B factor: 54.66
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M TRIS pH 8.5, 20% (w/w) PEG 2.000 MME, 0.01 M NiCl2
Matthews coefficient: 2.37
Solvent content (%): 48.1
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2020-06-03
IDO1 IN COMPLEX WITH COMPOUND 9 (PDB entry 7RRB)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 394 residues
Sequence: MISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.2093
R free: 0.2453
Average B factor: 82.451
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 MM TRIS PH 8.0, 20% (W/V) PEG6000, 0.2 M NACL
Matthews coefficient: 2.99
Solvent content (%): 58.83
Ligand: 3-[4-(6-cyclopropylpyridin-3-yl)phenyl]-N-(4-fluorophenyl)oxetane-3-carboxamide (6ZI)
Ligand formula: C24 H21 F N2 O2
Ligand molecular weight: 388.434
Ligand SMILES: c1cc(ccc1c2ccc(nc2)C3CC3)C4(COC4)C(=O)Nc5ccc(cc5)F
Ligand InChI: InChI=1S/C24H21FN2O2/c25-20-8-10-21(11-9-20)27-23(28)24(14-29-15-24)19-6-3-16(4-7-19)18-5-12-22(26-13-18)17-1-2-17/h3-13,17H,1-2,14-15H2,(H,27,28)
Release date: 2022-03-16
Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a (S)-methyl substitued Fasudil-derivative (PDB entry 5M75)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Cricetulus griseus
EC number: 2.7.11.11
Sequence length: 353 residues
Sequence: GHMGNAAAAKKGSEQESVKEFLAKAKEEFLKKWESPSQNTAQLDHFDRIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.538
R work: 0.1448
R free: 0.1739
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 277.15
Crystal growth procedure: Drop:
10 mg/ml PKA (0.240 mM)
30 mM MBT (MES/Bis-Tris Puffer pH 6.9)
1 mM DTT
0.1 mM EDTA
75 mM LiCl
0.03 mM Mega 8
0.07mM PKI (Sigma: P7739)
1.2 mM ligand solved in DMSO (50 mM Stock)

Reservoir: 18% Methanol

0.003 mL drop volume, 0.4 mL reservoir volume
Matthews coefficient: 2.18
Solvent content (%): 53.78
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: 2018-06-06