satarupa22/MacromolecularLigandDB huggingface dataset:
DDR1, 1-(1H-indazole-5-carbonyl)-5'-methoxy-1'-[2-oxo-2-[(2S)-2-(trifluoromethyl)pyrrolidin-1-yl]ethyl]spiro[piperidine-4,3'-pyrrolo[3,2-b]pyridine]-2'-one, 1.790A, P212121, Rfree=23.8% (PDB entry 6FIQ)
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): 1.79
R work: 0.199
R free: 0.2378
Average B factor: 40.7955
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 11.3 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed 1.3:1 with 90mM MES/NaOH pH6.5, 0.18M potassium iodide, 0.2M Li2SO4, 22.5% PEG 4K
Matthews coefficient: 2.14
Solvent content (%): 42.44
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2018-11-28
LSD1-CoREST in complex with T105 (PDB entry 8F6S)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.99.66
Sequence length: 871 residues
Sequence: GSSHHHHHHSSGLVPRGSHMLSGKKAAAAAAAAAAAATGTEAGPGTAGGSENGSEVAAQPAGLSGPAEVGPGAVGERTPRKKEPPRASPPGGLAEPPGSAGPQAGPTVVPGSATPMETGIAETPEGRRTSRRKRAKVEYREMDESLANLSEDEYYSEEERNAKAEKEKKLPPPPPQAPPEEENESEPEEPSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTLPRQATPGVPAQQSPSM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.91
R work: 0.2144
R free: 0.2443
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Matthews coefficient: 5.58
Solvent content (%): 77.96
Ligand: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-3-{3-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) (XHT)
Ligand formula: C40 H46 N12 O17 P2 S
Ligand molecular weight: 1060.876
Ligand SMILES: Cc1cc2c(cc1C)N3C(CC(C34C(=O)NC(=O)N=C4N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC5C(C(C(O5)n6cnc7c6ncnc7N)O)O)O)O)O)c8cccc(c8)C(=O)Nc9nnc(s9)C)O
Ligand InChI: InChI=1S/C40H46N12O17P2S/c1-16-7-22-23(8-17(16)2)52-27(55)10-21(19-5-4-6-20(9-19)34(59)45-39-49-48-18(3)72-39)40(52)36(46-38(61)47-37(40)60)50(22)11-24(53)29(56)25(54)12-66-70(62,63)69-71(64,65)67-13-26-30(57)31(58)35(68-26)51-15-44-28-32(41)42-14-43-33(28)51/h4-9,14-15,21,24-27,29-31,35,53-58H,10-13H2,1-3H3,(H,62,63)(H,64,65)(H2,41,42,43)(H,45,49,59)(H,47,60,61)/t21-,24+,25+,26-,27-,29-,30-,31-,35-,40+/m1/s1
Release date: 2024-06-12
Crystal Structure of human phosphodiesterase 10 in complex with 3-[2-(3-fluorophenyl)pyrazol-3-yl]-1-[3-(trifluoromethoxy)phenyl]pyridazin-4-one (PDB entry 5SKH)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1939
R free: 0.2368
Average B factor: 36.867
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: 2.61
Solvent content (%): 52.91
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: 2022-10-12
apo-Carbonic Anhydrase II soaked in 3NPA after UV at 90 K (PDB entry 7Y2K)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.12086
R free: 0.16314
Average B factor: 14.564
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 40.75
Release date: 2023-12-20
X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue (PDB entry 6EO7)
Macromolecule: GA68B2 - MODIFIED HUMAN THROMBIN BINDING APTAMER
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 15 residues
Sequence: GGTUGGTGTGGTTGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.16052
R free: 0.20848
Average B factor: 44.27
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 25% W/V PEG4000, 24% V/V 2-PROPANOL,
 0.2 M SODIUM CITRATE
Matthews coefficient: 4.19
Solvent content (%): 70.65
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2017-10-18
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000747a (PDB entry 5QGU)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.71
R work: 0.1986
R free: 0.2206
Average B factor: 32.177
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.3
Solvent content (%): 71.39
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: 2019-03-27
P38 alpha complex with AR117045 (PDB entry 6QDZ)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 362 residues
Sequence: GSMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.20346
R free: 0.2463
Average B factor: 27.854
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3000, Calcium Chloride, CHES
Matthews coefficient: 2.26
Solvent content (%): 45.65
Ligand: 2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine (I46)
Ligand formula: C14 H9 F2 N3
Ligand molecular weight: 257.238
Ligand SMILES: c1cc(ccc1c2c[nH]nc2c3ccnc(c3)F)F
Ligand InChI: InChI=1S/C14H9F2N3/c15-11-3-1-9(2-4-11)12-8-18-19-14(12)10-5-6-17-13(16)7-10/h1-8H,(H,18,19)
Release date: 2020-01-29
Human protein kinase CK2 alpha in complex with CK2-TN01 (PDB entry 8C6L)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 336 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1642
R free: 0.209
Average B factor: 26.1634
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 32% PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 1.98
Solvent content (%): 37.84
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: 2024-04-24
Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1) (PDB entry 7Z2L)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 405 residues
Sequence: MGSSHHHHHHSSGSAAYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSAALELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.56
R work: 0.1802
R free: 0.2441
Average B factor: 46.4
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 293
Crystal growth procedure: Well : 0.1M Phosphate buffer, pH= 6.2, PEG 3350 = 16%

Protein: 5mM Hepes, 200mM NaCl, 5mM DTT
Matthews coefficient: 2.83
Solvent content (%): 56.5
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2023-03-22
Carbonic Anhydrase II Complexed with 2-((3-Aminopropyl)(phenethyl)amino)-N-(furan-2-ylmethyl)-N-(4-sulfamoylphenethyl)acetamide (PDB entry 6WQ5)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.304
R work: 0.1602
R free: 0.1807
Average B factor: 18.0129
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M sodium citrate and 50mM Tris
Matthews coefficient: 2.09
Solvent content (%): 41.25
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: 2020-06-24
The crystal structure of TrkA(G595R) kinase in complex with N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide (PDB entry 8J5X)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: SDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHRDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09192247704
R work: 0.180103673153
R free: 0.220112735617
Average B factor: 37.7677335303
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.1M Na2HPO4/KH2PO4 (pH 6.2), 2M NaCl
Matthews coefficient: 2.62
Solvent content (%): 52.98
Ligand: N-(3-cyclopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-4^6-methyl-14-oxo-5-oxa-13-aza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclotetradecaphan-2-yne-4^5-carboxamide (A4U)
Ligand formula: C39 H45 N7 O3
Ligand molecular weight: 659.82
Ligand SMILES: Cc1c2cc(cc1C(=O)Nc3cc(cc(c3)C4CC4)CN5CCN(CC5)C)OCCCCCCCNC(=O)c6ccc7ncc(n7n6)C#C2
Ligand InChI: InChI=1S/C39H45N7O3/c1-27-30-10-11-33-25-41-37-13-12-36(43-46(33)37)39(48)40-14-6-4-3-5-7-19-49-34(23-30)24-35(27)38(47)42-32-21-28(20-31(22-32)29-8-9-29)26-45-17-15-44(2)16-18-45/h12-13,20-25,29H,3-9,14-19,26H2,1-2H3,(H,40,48)(H,42,47)
Release date: 2023-09-20
Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with human ACE2 (PDB entry 7EKH)
Macromolecule: Spike protein S1
Type: Protein, polypeptide(L)
Source organism: Severe acute respiratory syndrome coronavirus 2
Sequence length: 229 residues
Sequence: RVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLFRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2098
R free: 0.228
Average B factor: 45.67
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M MES, pH 6.5, 10% w/v PEG 5000 MME, 12% v/v1-Propanol
Matthews coefficient: 3.18
Solvent content (%): 61.31
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2021-11-03
CDK1/CyclinB1/CKS2 in complex with NU6102 (PDB entry 5LQF)
Macromolecule: Cyclin-dependent kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 302 residues
Sequence: GPLGSMEDYTKIEKIGEGTYGVVYKGRHKTTGQVVAMKKIRLESEEEGVPSTAIREISLLKELRHPNIVSLQDVLMQDSRLYLIFEFLSMDLKKYLDSIPPGQYMDSSLVKSYLYQILQGIVFCHSRRVLHRDLKPQNLLIDDKGTIKLADFGLARAFGIPIRVYTHEVVTLWYRSPEVLLGSARYSTPVDIWSIGTIFAELATKKPLFHGDSEIDQLFRIFRALGTPNNEVWPEVESLQDYKNTFPKWKPGSLASHVKNLDENGLDLLSKMLIYDPAKRISGKMALNHPYFNDLDNQIKKM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.19764
R free: 0.25385
Average B factor: 47.072
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M MES/IMIDAZOLE BUFFER (PH6.7),     6.5% MPD, 5% PEG4K, 10% PEG1K PROTEIN AT 10-12 MG/ML
Matthews coefficient: 2.39
Solvent content (%): 48.46
Ligand: O6-CYCLOHEXYLMETHOXY-2-(4'-SULPHAMOYLANILINO) PURINE (4SP)
Ligand formula: C18 H22 N6 O3 S
Ligand molecular weight: 402.471
Ligand SMILES: c1cc(ccc1Nc2nc3c(c(n2)OCC4CCCCC4)nc[nH]3)S(=O)(=O)N
Ligand InChI: InChI=1S/C18H22N6O3S/c19-28(25,26)14-8-6-13(7-9-14)22-18-23-16-15(20-11-21-16)17(24-18)27-10-12-4-2-1-3-5-12/h6-9,11-12H,1-5,10H2,(H2,19,25,26)(H2,20,21,22,23,24)
Release date: 2017-01-11
JAK3 with Cyanamide CP23 (PDB entry 6DB3)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 321 residues
Sequence: MGHHHHHHQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGCERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSRGCETHAFTAHPEGKHHSLSFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.1886
R free: 0.2236
Average B factor: 41.19
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 0.2M (NH4)2SO4, 2% phenylurea
Matthews coefficient: 2.25
Solvent content (%): 45.41
Ligand: [(1S)-1-methyl-6-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-inden-1-yl]cyanamide (G54)
Ligand formula: C17 H15 N5
Ligand molecular weight: 289.335
Ligand SMILES: CC1(CCc2c1cc(cc2)c3c4cc[nH]c4ncn3)NC#N
Ligand InChI: InChI=1S/C17H15N5/c1-17(22-9-18)6-4-11-2-3-12(8-14(11)17)15-13-5-7-19-16(13)21-10-20-15/h2-3,5,7-8,10,22H,4,6H2,1H3,(H,19,20,21)/t17-/m0/s1
Release date: 2018-11-28
Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-001 (PDB entry 8FH5)
Macromolecule: Aldo-keto reductase family 1 member B1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.300
Sequence length: 315 residues
Sequence: ASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.143
R free: 0.1672
Average B factor: 14.03
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG 3350, 100 mM Bis-Tris
Matthews coefficient: 2.21
Solvent content (%): 44.5
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2023-12-20
Crystal Structure of Drosophila DHX36 helicase in complex with ssDNA CpG_A (PDB entry 5N9F)
Macromolecule: CG9323, isoform A
Type: Protein, polypeptide(L)
Source organism: Drosophila melanogaster
EC number: 3.6.1.3
Sequence length: 944 residues
Sequence: MQRDRDSSGSNARKGNRPPGLRGKDIGLYYRNLARQQKKDRGENAESKEPQIRLGCNVSAPSGVLERVKELMEDYSRAPSRQNVDDKNVDAKFQQQFRHLLSVNFEEFVAETKERNADLDWVNPKLDERLQLELGQRQLEENAKKRLEARKKLPTMKYADDIIQAVRENQVILIVGSTGCGKTTQVPQILLDDAISRGCASSCRIICTQPRRISAIAIAEWVSYERCESLGNSVGYQIRLESRKARERASITYCTTGVLLQQLQSDPLMHNLSVLILDEIHERSVETDLLMGLLKVILPHRPDLKVILMSATVREQDFCDYFNNCPMFRIEGVMFPVKMLYLEDVLSKTNYEFQKFRDRRPKRDPPERRMKHEAMIEPYLRRIRNSYDSRVLDKLRLPESEGCEDIDFIADLVYYICENEPEGAILVFLPGYDKISQLYNILDKPKTSKGQRWRDHMAVFPLHSLMQSGEQQAVFRRPPAGQRKVIISTIIAETSVTIDDVVYVINSGRTKATNYDIETNIQSLDEVWVTKANTQQRRGRAGRVRPGICYNLFSRAREDRMDDIPTPEILRSKLESIILSLKLLHIDDPYRFLQTLINAPNPEAIKMGVELLKRIEALDQTGTLTPLGMHLAKLPIDPQMGKMILMSALFCCLDPITSAAAALSFKSPFYSPLGKESRVDEIKRRMARNMRSDHLMVHNTIIAYRDSRYSHAERDFCYKNFLSSMTLQQLERMKNQFSELLYNYKFLASSNCKDAASNKNSEKIPLLRAIIGAGLYPNMAHLRKSRQIKNRVRAIHTMATDDGRRVNFHPSSVNSGESGFDSAYFVYFQRQKSTDLFLLDSTMVFPMALIIFGDGVEAGVTQNTPYLCVAKTYYFKCNRETADVVIQLRSNLEKLLLKKALYPAPIEENGYEKQLIKAIELLLSLDERLGEDYISSDEIDDIVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.969
R work: 0.2142
R free: 0.2696
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MES monohydrate-imidazole
20mM sodium formate
20mM ammonium acetate
20mM sodium citrate tribasic hydrate
20mM sodium oxamate
20mM potassium sodium tartrate tetrahydrate
Matthews coefficient: 2.69
Solvent content (%): 54.3
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-03-21
ATAD2 in complex with FragLite6 (PDB entry 7QWO)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2392
R free: 0.2725
Average B factor: 41.941
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
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: 2022-11-23