satarupa22/MacromolecularLigandDB huggingface dataset:
BACE1 compound 23 (PDB entry 6EJ3)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 501 residues
Sequence: MAQALPWLLLWMGAGVLPAHGTQHGIRLPLRSGLGGAPLGLRLPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDESTLMTIAYVMAAICALFMLPLCLMVCQWRCLRCLRQQHDDFADDISLLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.194
R free: 0.217
Average B factor: 54.91
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 11% PEG 6k, 100mM NaOAc pH 5.0
Matthews coefficient: 3.09
Solvent content (%): 60.22
Ligand: (1r,4r)-4-methoxy-6'-(5-methyl-3-pyridinyl)-3'H-dispiro[cyclohexane-1,2'-indene-1',4''-[1,3]oxazol]-2''-amine (B7T)
Ligand formula: C23 H27 N3 O2
Ligand molecular weight: 377.479
Ligand SMILES: Cc1cc(cnc1)c2ccc3c(c2)C4(COC(=N4)N)C5(C3)CCC(CC5)OC
Ligand InChI: InChI=1S/C23H27N3O2/c1-15-9-18(13-25-12-15)16-3-4-17-11-22(7-5-19(27-2)6-8-22)23(20(17)10-16)14-28-21(24)26-23/h3-4,9-10,12-13,19H,5-8,11,14H2,1-2H3,(H2,24,26)/t19-,22-,23-/m0/s1
Release date: 2018-04-18
PanDDA analysis group deposition -- Crystal Structure of human PARP14 Macrodomain 3 in complex with FMOPL000597a (PDB entry 5QI6)
Macromolecule: Poly [ADP-ribose] polymerase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2
Sequence length: 183 residues
Sequence: SMFYGTVSSPDSGVYEMKIGSIIFQVASGDITKEEADVIVNSTSNSFNLKAGVSKAILECAGQNVERECSQQAQQRKNDYIITGGGFLRCKNIIHVIGGNDVKSSVSSVLQECEKKNYSSICLPAIGTGNAKQHPDKVAEAIIDAIEDFVQKGSAQSVKKVKVVIFLPQVLDVFYANMKKREG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1938
R free: 0.21
Average B factor: 14.772
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 277
Crystal growth procedure: 80 mM KBr, 30 % PEG2kMME
Matthews coefficient: 2.01
Solvent content (%): 38.85
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: 2019-04-10
HUMAN VH1-RELATED DUAL-SPECIFICITY PHOSPHATASE (VHR) complexed with 2-((2,4-difluorobenzyl)amino)-2-oxoacetic acid (PDB entry 8TK2)
Macromolecule: Dual specificity protein phosphatase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 183 residues
Sequence: GSFELSVQDLNDLLSDGSGCYSLPSQPCNEVTPRIYVGNASVAQDIPKLQKLGITHVLNAAEGRSFMHVNTNANFYKDSGITYLGIKANDTQEFNLSAYFERAADFIDQALAQKNGRVLVHCREGYSRSPTLVIAYLMMRQKMDVKSALSIVRQNREIGPNDGFLAQLCQLNDRLAKEGKLKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.17587
R free: 0.22265
Average B factor: 29.235
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: Protein-compound mixture in 50 mM TRIS-Cl pH 8.5, 1 mM TCEP, 0.5 mM EDTA, 5% DMSO were mixed with the precipitant solution (100 mM Bis-Tris pH 6.5, 50 mM NH4F, 28% (w/v) PEGME-2000) and equilibrated against the precipitant solution.
Matthews coefficient: 2.25
Solvent content (%): 45.32
Ligand: {[(2,4-difluorophenyl)methyl]amino}(oxo)acetic acid (I1Y)
Ligand formula: C9 H7 F2 N O3
Ligand molecular weight: 215.154
Ligand SMILES: c1cc(c(cc1F)F)CNC(=O)C(=O)O
Ligand InChI: InChI=1S/C9H7F2NO3/c10-6-2-1-5(7(11)3-6)4-12-8(13)9(14)15/h1-3H,4H2,(H,12,13)(H,14,15)
Release date: 2024-08-14
Crystal structure of human METTL1 in complex with SAH (PDB entry 7OGJ)
Macromolecule: tRNA (guanine-N(7)-)-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.33
Sequence length: 252 residues
Sequence: MHHHHHHSSGRENLYFQGDHTLRYPVKPEEMDWSELYPEFFAPLTQNQSHDDPKDKKEKRAQAQVEFADIGCGYGGLLVELSPLFPDTLILGLEIRVKVSDYVQDRIRALRAAPAGGFQNIACLRSNAMKHLPNFFYKGQLTKMFFLFPDPHFKRTKHKWRIISPTLLAEYAYVLRVGGLVYTITDVLELHDWMCTHFEEHPLFERVPLEDLSEDPVVGHLGTSTEEGKKVLRNGGKNFPAIFRRIQDPVLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.59
R work: 0.1933
R free: 0.2147
Average B factor: 31.22
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 200 mM lithium sulfate, 20% PEG 1000, 100 mM phosphate-citrate buffer pH 4.2
Matthews coefficient: 3.03
Solvent content (%): 59.39
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: 2021-05-19
MST3 IN COMPLEX WITH SUNITINIB (PDB entry 4QMZ)
Macromolecule: SERINE/THREONINE-PROTEIN KINASE 24
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: GPLGSEFMAHSPVQSGLPGMQNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQKVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHSEKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKVLFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQSHDDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1676
R free: 0.2241
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 12.5 mg/mL MST3, 1 mM SUNITINIB, 25 mM TRIS, PH 8.0, 50 MM HEPES, 125 mM SODIUM CHLORIDE, 100 mM MAGNESIUM CHLORIDE, 15% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.13
Solvent content (%): 42.24
Ligand: N-[2-(diethylamino)ethyl]-5-[(Z)-(5-fluoro-2-oxo-1,2-dihydro-3H-indol-3-ylidene)methyl]-2,4-dimethyl-1H-pyrrole-3-carbo
xamide (B49)
Ligand formula: C22 H27 F N4 O2
Ligand molecular weight: 398.474
Ligand SMILES: CCN(CC)CCNC(=O)c1c(c([nH]c1C)C=C2c3cc(ccc3NC2=O)F)C
Ligand InChI: InChI=1S/C22H27FN4O2/c1-5-27(6-2)10-9-24-22(29)20-13(3)19(25-14(20)4)12-17-16-11-15(23)7-8-18(16)26-21(17)28/h7-8,11-12,25H,5-6,9-10H2,1-4H3,(H,24,29)(H,26,28)/b17-12-
Release date: 2015-07-01
Crystal structure of compound 2 bound to CK2alpha (PDB entry 7ZY5)
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): 1.82
R work: 0.1989
R free: 0.2191
Average B factor: 40.86
Crystallization method: VAPOR DIFFUSION, SITTING 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: 2.23
Solvent content (%): 44.86
Ligand: 1-NAPHTHOL (1NP)
Ligand formula: C10 H8 O
Ligand molecular weight: 144.17
Ligand SMILES: c1ccc2c(c1)cccc2O
Ligand InChI: InChI=1S/C10H8O/c11-10-7-3-5-8-4-1-2-6-9(8)10/h1-7,11H
Release date: 2022-10-12
RIP2 kinase catalytic domain complex with (5S,6S,8R)-2-(benzo[d]thiazol-5-yl)-6-hydroxy-4,5,6,7,8,9-hexahydro-5,8-methanopyrazolo[1,5-a][1,3]diazocine-3-carboxamide (PDB entry 6UL8)
Macromolecule: Receptor-interacting serine/threonine-protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 306 residues
Sequence: AISSALPTIPYHKLADLRYLSRGASGTVSSARHADWRVQVAVKHLHIHTPLLDSERKDVLREAEILHKARFSYILPILGICNEPEFLGIVTEYMPNGSLNELLHRKTEYPDVAWPLRFRILHEIALGVNYLHNMTPPLLHHDLKTQNILLDNEFHVKIADFGLCKWRMMSLSQSRSSKSAPEGGTIIYMPPENYEPGQKSRASIKHDIYSYAVITWEVLSRKQPFEDVTNPLQIMYSVSQGHRPVINEESLPYDIPHRARMISLIESGWAQNPDERPSFLKCLIELEPVLRTFEEITFLEAVIQLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.1831
R free: 0.22
Average B factor: 65.189
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 85 mM Tris, pH 7.5, 200 mM calcium chloride, 10% PEG400, 5% glycerol, in 24 well Linbro trays at 22 degrees C. Crystals were frozen directly from the tray using paraffin oil as a cryoprotectant.
Matthews coefficient: 3.71
Solvent content (%): 66.85
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: 2019-12-04
Human Argonaute2 Bound to an siRNA (PDB entry 5JS1)
Macromolecule: Protein argonaute-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26
Sequence length: 859 residues
Sequence: MYSGAGPALAPPAPPPPIQGYAFKPPPRPDFGTSGRTIKLQANFFEMDIPKIDIYHYELDIKPEKCPRRVNREIVEHMVQHFKTQIFGDRKPVFDGRKNLYTAMPLPIGRDKVELEVTLPGEGKDRIFKVSIKWVSCVSLQALHDALSGRLPSVPFETIQALDVVMRHLPSMRYTPVGRSFFTASEGCSNPLGGGREVWFGFHQSVRPSLWKMMLNIDVSATAFYKAQPVIEFVCEVLDFKSIEEQQKPLTDSQRVKFTKEIKGLKVEITHCGQMKRKYRVCNVTRRPASHQTFPLQQESGQTVECTVAQYFKDRHKLVLRYPHLPCLQVGQEQKHTYLPLEVCNIVAGQRCIKKLTDNQTSTMIRATARSAPDRQEEISKLMRSADFNTDPYVREFGIMVKDEMTDVTGRVLQPPSILYGGRNKAIATPVQGVWDMRNKQFHTGIEIKVWAIACFAPQRQCTEVHLKSFTEQLRKISRDAGMPIQGQPCFCKYAQGADSVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQRTTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIAAVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRDGVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKSGNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQLCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQALAKAVQVHQDTLRTMYFA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.499
R work: 0.2165
R free: 0.2475
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG 3350, 50mM Phenol, 10% Isopropanol, 5mM Magnesium Chloride, 100mM Tris
Matthews coefficient: 2.19
Solvent content (%): 43.78
Ligand: PHENOL (IPH)
Ligand formula: C6 H6 O
Ligand molecular weight: 94.111
Ligand SMILES: c1ccc(cc1)O
Ligand InChI: InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
Release date: 2016-07-20
Crystal structure of the catalytic-domain of human carbonic anhydrase IX at 1.6 angstrom resolution (PDB entry 5DVX)
Macromolecule: Carbonic anhydrase 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: HWRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELSGFQLPPLPELRLRNNGHSVQLTLPPGLEMKLGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVHLSTKYARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDISALLPSDFSRYFQYEGSLTTPPCAQGVIWTVFNQTVSLSAKQLHTLSDTLWGPGDSRLQLNFRATQPLNGRVIEASFPAGVDSSPR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.598
R work: 0.1678
R free: 0.1913
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 0.1 M Tris HCl, pH 8.5, 8% (w/v) PEG 8000
Matthews coefficient: 2.84
Solvent content (%): 56.69
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: 2016-08-03
Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, circular permutant P1/2 (PDB entry 5J07)
Macromolecule: Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn],Superoxide dismutase [Cu-Zn]
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.15.1.1
Sequence length: 115 residues
Sequence: APVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHGAGGDLGNVTADKDGVADVSIEDSVISLSGDHSIIGRTLVVHEKAGAGAGSRLASGVIGIAQAGAGATKAVAVLKGDG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1927
R free: 0.2306
Average B factor: 49.806
Crystallization method: EVAPORATION
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MIB buffer
pH 5.0
25 % w/v PEG 1500
Matthews coefficient: 2.12
Solvent content (%): 41.95
Release date: 2017-02-01
CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-29 A.K.A 7-(1,2-DIPHENYLETHYL)-1H-[1,2,3]TRIAZOLO[4,5-B]PYRIDIN-5-AMINE (PDB entry 6WXZ)
Macromolecule: Myeloperoxidase light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.2.2
Sequence length: 105 residues
Sequence: CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.226
R work: 0.2107
R free: 0.2419
Average B factor: 58.81
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen
Matthews coefficient: 2.65
Solvent content (%): 53.55
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: 2020-10-14
Crystal structure of JAK2 JH2-R683S (PDB entry 8C0A)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: VFHKIRNEDLIFNESLGQGTFTKIFKGVRREVGDYGQLHETEVLLKVLDKAHRNYSESFFEAASMMSKLSHKHLVLNYGVCVCGDENILVQEFVKFGSLDTYLKKNKNCINILWKLEVAKQLAAAMHFLEENTLIHGNVCAKNILLISEEDRKTGNPPFIKLSDPGISITVLPKDILQERIPWVPPECIENPKNLNLATDKWSFGTTLWEICSGGDKPLSALDSQRKLQFYEDRHQLPAPKAAELANLINNCMDYEPDHRPSFRAIIRDLNSLFTPDLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.194
R free: 0.2375
Average B factor: 30.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris pH 8.0, 21% PEG4000, 0.1M Na-acetate
Matthews coefficient: 2.22
Solvent content (%): 44.67
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: 2023-12-27
Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine. (PDB entry 6QSW)
Macromolecule: Complement factor B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.47
Sequence length: 291 residues
Sequence: SLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.1567
R free: 0.1881
Average B factor: 21.87
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.0 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6), 2 mM inhibitor
Matthews coefficient: 2.74
Solvent content (%): 55.13
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: 2019-03-27
Crystal structures of human E-NPP 1: apo (PDB entry 6WFJ)
Macromolecule: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.1
Sequence length: 925 residues
Sequence: MERDGCAGGGSRGGEGGRAPREGPAGNGRDRGRSHAAEAPGDPQAAASLLAPMDVGEEPLEKAARARTAKDPNTYKVLSLVLSVCVLTTILGCIFGLKPSCAKEVKSCKGRCFERTFGNCRCDAACVELGNCCLDYQETCIEPEHIWTCNKFRCGEKRLTRSLCACSDDCKDKGDCCINYSSVCQGEKSWVEEPCESINEPQCPAGFETPPTLLFSLDGFRAEYLHTWGGLLPVISKLKKCGTYTKNMRPVYPTKTFPNHYSIVTGLYPESHGIIDNKMYDPKMNASFSLKSKEKFNPEWYKGEPIWVTAKYQGLKSGTFFWPGSDVEINGIFPDIYKMYNGSVPFEERILAVLQWLQLPKDERPHFYTLYLEEPDSSGHSYGPVSSEVIKALQRVDGMVGMLMDGLKELNLHRCLNLILISDHGMEQGSCKKYIYLNKYLGDVKNIKVIYGPAARLRPSDVPDKYYSFNYEGIARNLSCREPNQHFKPYLKHFLPKRLHFAKSDRIEPLTFYLDPQWQLALNPSERKYCGSGFHGSDNVFSNMQALFVGYGPGFKHGIEADTFENIEVYNLMCDLLNLTPAPNNGTHGSLNHLLKNPVYTPKHPKEVHPLVQCPFTRNPRDNLGCSCNPSILPIEDFQTQFNLTVAEEKIIKHETLPYGRPRVLQKENTICLLSQHQFMSGYSQDILMPLWTSYTVDRNDSFSTEDFSNCLYQDFRIPLSPVHKCSFYKNNTKVSYGFLSPPQLNKNSSGIYSEALLTTNIVPMYQSFQVIWRYFHDTLLRKYAEERNGVNVVSGPVFDFDYDGRCDSLENLRQKRRVIRNQEILIPTHFFIVLTSCKDTSQTPLHCENLDTLAFILPHRTDNSESCVHGKHDSSWVEELLMLHRARITDVEHITGLSFYQQRKEPVSDILKLKTHLPTFSQED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1994
R free: 0.2223
Average B factor: 60.345
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 7.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate
Matthews coefficient: 3.3
Solvent content (%): 62.67
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-09-09
PanDDA analysis group deposition of ground-state model of PTP1B, using pre-clustering, cluster3 (PDB entry 7GTY)
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): 1.54
R work: 0.197
R free: 0.2213
Average B factor: 39.0877
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: 3.34
Solvent content (%): 63.13
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: 2024-01-31
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 4b (PDB entry 5NKI)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.675
R work: 0.1604
R free: 0.1894
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD/PEG1000/PEG3350 (MD), 0.1 M Amino Acids Mix (MD), 0.1 M Hepes pH6.5
Matthews coefficient: 1.94
Solvent content (%): 36.45
Ligand: ~{N}-(2-chloranyl-6-methyl-phenyl)-2-[(3-methylsulfonyl-5-morpholin-4-yl-phenyl)amino]-1,3-thiazole-5-carboxamide (8ZW)
Ligand formula: C22 H23 Cl N4 O4 S2
Ligand molecular weight: 507.025
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cc(cc(c3)S(=O)(=O)C)N4CCOCC4)Cl
Ligand InChI: InChI=1S/C22H23ClN4O4S2/c1-14-4-3-5-18(23)20(14)26-21(28)19-13-24-22(32-19)25-15-10-16(27-6-8-31-9-7-27)12-17(11-15)33(2,29)30/h3-5,10-13H,6-9H2,1-2H3,(H,24,25)(H,26,28)
Release date: 2017-06-07
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1137725943 (PDB entry 7G86)
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): 1.699
R work: 0.2007
R free: 0.2293
Average B factor: 30.79
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: 2.53
Solvent content (%): 51.46
Ligand: N-[(1H-indol-4-yl)methyl]ethanamine (YXB)
Ligand formula: C11 H14 N2
Ligand molecular weight: 174.242
Ligand SMILES: CCNCc1cccc2c1cc[nH]2
Ligand InChI: InChI=1S/C11H14N2/c1-2-12-8-9-4-3-5-11-10(9)6-7-13-11/h3-7,12-13H,2,8H2,1H3
Release date: 2023-07-12
Crystal structure of human carbonic anhydrase isozyme II with 4-chloro-2-cyclohexylsulfanyl-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide (PDB entry 6R6F)
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): 1.2
R work: 0.1457
R free: 0.185
Average B factor: 19.0325
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)
Matthews coefficient: 2.11
Solvent content (%): 41.82
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: 2019-12-18