satarupa22/MacromolecularLigandDB huggingface dataset:
STRUCTURE OF THE HUMAN TELOMERASE THUMB DOMAIN (PDB entry 5UGW)
Macromolecule: Telomerase reverse transcriptase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.49
Sequence length: 175 residues
Sequence: SNANRGFKAGRNMRRKLFGVLRLKCHSLFLDLQVNSLQTVCTNIYKILLLQAYRFHACVLQLPFHQQVWKNPTFFLRVISDTASLCYSILKAKNAGMSLGAKGAAGPLPSEAVQWLCHQAFLLKLTRHRVTYVPLLGSLRTAQTQLSRKLPGTTLTALEAAANPALPSDFKTILD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.31
R work: 0.19729
R free: 0.209
Average B factor: 61.161
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 283
Crystal growth procedure: 50 mM Tris 8.5
0.8 M LiSo4
10 mM GSH/GSSG
3% 1,6-hexanediol
Matthews coefficient: 3.22
Solvent content (%): 61.79
Ligand: GLUTATHIONE (GSH)
Ligand formula: C10 H17 N3 O6 S
Ligand molecular weight: 307.323
Ligand SMILES: C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)N
Ligand InChI: InChI=1S/C10H17N3O6S/c11-5(10(18)19)1-2-7(14)13-6(4-20)9(17)12-3-8(15)16/h5-6,20H,1-4,11H2,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1
Release date: 2017-02-08
compound 1a bound KMT9 crystal structure (PDB entry 8QDG)
Macromolecule: Methyltransferase N6AMT1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 203 residues
Sequence: SHVGRGAFSDVYEPAEDTFLLLDALEAAAAELAGVEICLEVGSGSGVVSAFLASMIGPQALYMCTDINPEAAACTLETARCNKVHIQPVITDLVKGLLPRLTEKVDLLVFNPPYVVTPPQEVGSHGIEAAWAGGRNGREVMDRFFPLVPDLLSPRGLFYLVTIKENNPEEILKIMKTKGLQGTTALSRQAGQETLSVLKFTKS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.392
R work: 0.1521
R free: 0.1794
Average B factor: 22.209
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 1.2 M Na3Citrate, 0.1M Tris 7.5
Matthews coefficient: 3.16
Solvent content (%): 61.02
Ligand: (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[(3~{S})-pyrrolidin-3-yl]amino]-2-azanyl-butanoic acid (SDU)
Ligand formula: C18 H28 N8 O5
Ligand molecular weight: 436.466
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)O)N)C4CCNC4)O)O)N
Ligand InChI: InChI=1S/C18H28N8O5/c19-10(18(29)30)2-4-25(9-1-3-21-5-9)6-11-13(27)14(28)17(31-11)26-8-24-12-15(20)22-7-23-16(12)26/h7-11,13-14,17,21,27-28H,1-6,19H2,(H,29,30)(H2,20,22,23)/t9-,10-,11+,13+,14+,17+/m0/s1
Release date: 2024-09-11
Discovery and Preclinical Pharmacology of INE963, A Potent and Fast-Acting Blood-Stage Antimalarial with a High Barrier to Resistance and Potential for Single-Dose Cure in Uncomplicated Malaria (PDB entry 7SQM)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: GPGSPLNTLSISNKKASDAEKVYGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1734
R free: 0.2046
Average B factor: 26.61
Crystallization method: EVAPORATION
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M NA CITRATE PH5, 20% PEG6K
Matthews coefficient: 3.01
Solvent content (%): 59.08
Ligand: 1-[(4S)-5-(2,4-difluorophenyl)imidazo[2,1-b][1,3,4]thiadiazol-2-yl]-4-methylpiperidin-4-amine (A5G)
Ligand formula: C16 H17 F2 N5 S
Ligand molecular weight: 349.401
Ligand SMILES: CC1(CCN(CC1)c2nn3c(cnc3s2)c4ccc(cc4F)F)N
Ligand InChI: InChI=1S/C16H17F2N5S/c1-16(19)4-6-22(7-5-16)15-21-23-13(9-20-14(23)24-15)11-3-2-10(17)8-12(11)18/h2-3,8-9H,4-7,19H2,1H3
Release date: 2021-12-29
Crystal Structure of human phosphodiesterase 10 in complex with 5,8-dimethyl-2-[2-[2-methyl-5-(2-methylpyrrolidin-1-yl)-1,2,4-triazol-3-yl]ethyl]-[1,2,4]triazolo[1,5-a]pyrazine (PDB entry 5SFI)
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): 2.01
R work: 0.1699
R free: 0.2281
Average B factor: 37.874
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: 2.63
Solvent content (%): 53.21
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: 2022-10-12
Human Carbonic Anhydrase II complexed with AceK (PDB entry 5WG7)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1418
R free: 0.1761
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6 M sodium citrate and 50 mM Tris
Matthews coefficient: 2.1
Solvent content (%): 41.53
Ligand: Acesulfame (AUD)
Ligand formula: C4 H5 N O4 S
Ligand molecular weight: 163.152
Ligand SMILES: CC1=CC(=O)NS(=O)(=O)O1
Ligand InChI: InChI=1S/C4H5NO4S/c1-3-2-4(6)5-10(7,8)9-3/h2H,1H3,(H,5,6)
Release date: 2018-02-07
Crystal structure of the C-terminal domain of human N-acetylglucosaminyltransferase IVa (PDB entry 7XTL)
Macromolecule: Alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A soluble form
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.145
Sequence length: 172 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASKIHVNPPAEVSTSLKVYQGHTLEKTYMGEDFFWAITPIAGDYILFKFDKPVNVESYLFHSGNQEHPGDILLNTTVEVLPFKSEGLEISKETKDKRLEDGYFRIGKFENGVAEGMVDPSLNPISAFRLSVIQNSAVWAILNEIHIKKATN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.972
R work: 0.2204
R free: 0.2663
Average B factor: 61.557
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M lithium nitrate, 20%(w/v) PEG3350
Matthews coefficient: 1.82
Solvent content (%): 32.58
Release date: 2022-09-28
Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase (PDB entry 5M4M)
Macromolecule: [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.2
Sequence length: 408 residues
Sequence: MRWVWALLKNASLAGSAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDGSTNPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTAPTPQPGTGGTPLAGFGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYQTIQEAGDWCVPSTEPKNTSTYRVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.21663
R free: 0.2617
Average B factor: 59.832
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M SODIUM ACETATE PH 5.8
0.125 M MAGNESIUM CHLORIDE
6% ISOPROPANOL
Matthews coefficient: 3.08
Solvent content (%): 60.06
Ligand: ~{N}-[4-[methyl(quinoxalin-6-ylmethyl)carbamoyl]phenyl]-2,4-bis(oxidanyl)-~{N}-(phenylmethyl)benzamide (7FW)
Ligand formula: C31 H26 N4 O4
Ligand molecular weight: 518.563
Ligand SMILES: CN(Cc1ccc2c(c1)nccn2)C(=O)c3ccc(cc3)N(Cc4ccccc4)C(=O)c5ccc(cc5O)O
Ligand InChI: InChI=1S/C31H26N4O4/c1-34(19-22-7-14-27-28(17-22)33-16-15-32-27)30(38)23-8-10-24(11-9-23)35(20-21-5-3-2-4-6-21)31(39)26-13-12-25(36)18-29(26)37/h2-18,36-37H,19-20H2,1H3
Release date: 2017-02-22
Notum fragment 5e (PDB entry 7BM7)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.2193
R free: 0.2549
Average B factor: 32.8788
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.92
Solvent content (%): 36.01
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: 2022-03-02
Crystal Structure of a FVIIa-Trypsin Chimera (FT) in Complex with Soluble Tissue Factor (PDB entry 4YLQ)
Macromolecule: Coagulation factor VII
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 152 residues
Sequence: ANAFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISYSDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKRNASKPQGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1397
R free: 0.1737
Average B factor: 26.4558
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 295
Crystal growth procedure: 0.1M NaCitrate, 16.6% PEG 3350, 12.5% 1-Propanol, with seeding
Matthews coefficient: 2.52
Solvent content (%): 51.23
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: 2015-12-30
CDK8-CYCC IN COMPLEX WITH (3-Amino-1H-indazol-5-yl)-[(S)-2-(4-fluoro-phenyl)-piperidin-1-yl]-methanone (PDB entry 5IDP)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 370 residues
Sequence: DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.23098
R free: 0.27232
Average B factor: 46.549
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.2 M sodium formate, pH 6.9
Matthews coefficient: 3.08
Solvent content (%): 60.13
Ligand: (3-amino-1H-indazol-5-yl)[(2S)-2-(4-fluorophenyl)piperidin-1-yl]methanone (6A6)
Ligand formula: C19 H19 F N4 O
Ligand molecular weight: 338.379
Ligand SMILES: c1cc(ccc1C2CCCCN2C(=O)c3ccc4c(c3)c(n[nH]4)N)F
Ligand InChI: InChI=1S/C19H19FN4O/c20-14-7-4-12(5-8-14)17-3-1-2-10-24(17)19(25)13-6-9-16-15(11-13)18(21)23-22-16/h4-9,11,17H,1-3,10H2,(H3,21,22,23)/t17-/m0/s1
Release date: 2016-12-21
Crystal Structure of D181A/R192F hFen1 in complex with DNA (PDB entry 5ZOF)
Macromolecule: Flap endonuclease 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 333 residues
Sequence: MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDMACLTFGSPVLMFHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.249
R work: 0.2353
R free: 0.2688
Average B factor: 56.5319
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: PEG 3350, MgCl2, Tris, KCl
Matthews coefficient: 2.28
Solvent content (%): 46.01
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2019-01-30
Crystal structure of human heparanase in complex with heparin tetrasaccharide dp4 (PDB entry 5E9C)
Macromolecule: Heparanase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.166
Sequence length: 389 residues
Sequence: DPGKKFKNSTYSRSSVDVLYTFANCSGLDLIFGLNALLRTADLQWNSSNAQLLLDYCSSKGYNISWELGNEPNSFLKKADIFINGSQLGEDFIQLHKLLRKSTFKNAKLYGPDVGQPRRKTAKMLKSFLKAGGEVIDSVTWHHYYLNGRTATREDFLNPDVLDIFISSVQKVFQVVESTRPGKKVWLGETSSAYGGGAPLLSDTFAAGFMWLDKLGLSARMGIEVVMRQVFFGAGNYHLVDENFDPLPDYWLSLLFKKLVGTKVLMASVQGSKRRKLRVYLHCTNTDNPRYKEGDLTLYAINLHNVTKYLRLPYPFSNKQVDKYLLRPLGPHGLLSKSVQLNGLTLKMVDDQTLPPLMEKPLRPGSSLGLPAFSYSFFVIRNAKVAACI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.17208
R free: 0.2105
Average B factor: 36.573
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MES pH 5.5, 0.1 M MgCl2, 17% PEG3350
Matthews coefficient: 2.46
Solvent content (%): 50.02
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: 2015-11-18
Structure of DYRK1A in complex with compound 50 (PDB entry 7AKL)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 359 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMIVKNGEKWMDRYEIDSLIGKGSFGQVVKAYDRVEQEWVAIKIIKNKKAFLNQAQIEVRLLELMNKHDTEMKYYIVHLKRHFMFRNHLCLVFEMLSYNLYDLLRNTNFRGVSLNLTRKFAQQMCTALLFLATPELSIIHCDLKPENILLCNPKRSAIKIVDFGSSCQLGQRIYQYIQSRFYRSPEVLLGMPYDLAIDMWSLGCILVEMHTGEPLFSGANEVDQMNKIVEVLGIPPAHILDQAPKARKFFEKLPDGTWNLKKTKDGKREYKPPGTRKLHNILGVETGGPGGRRAGESGHTVADYLKFKDLILRMLDYDPKTRIQPYYALQHSFFKKTADE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.167
R free: 0.2102
Average B factor: 27.351
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG3350, 0.1M MES buffer pH6.5, 0.2M MgCl2
Matthews coefficient: 2.5
Solvent content (%): 50.75
Ligand: 4-(2,3-dimethyl-1-benzofuran-5-yl)pyridine-2,6-diamine (RK5)
Ligand formula: C15 H15 N3 O
Ligand molecular weight: 253.299
Ligand SMILES: Cc1c(oc2c1cc(cc2)c3cc(nc(c3)N)N)C
Ligand InChI: InChI=1S/C15H15N3O/c1-8-9(2)19-13-4-3-10(5-12(8)13)11-6-14(16)18-15(17)7-11/h3-7H,1-2H3,(H4,16,17,18)
Release date: 2021-05-26
Human atlastin-1 (residues 1-439) bound to GDP-Mg2+ exhibits an ordered amino terminus (PDB entry 6XJN)
Macromolecule: Atlastin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 439 residues
Sequence: MAKNRRDRNSWGGFSEKTYEWSSEEEEPVKKAGPVQVLIVKDDHSFELDETALNRILLSEAVRDKEVVAVSVAGAFRKGKSFLMDFMLRYMYNQESVDWVGDYNEPLTGFSWRGGSERETTGIQIWSEIFLINKPDGKKVAVLLMDTQGTFDSQSTLRDSATVFALSTMISSIQVYNLSQNVQEDDLQHLQLFTEYGRLAMEETFLKPFQSLIFLVRDWSFPYEFSYGADGGAKFLEKRLKVSGNQHEELQNVRKHIHSCFTNISCFLLPHPGLKVATNPNFDGKLKEIDDEFIKNLKILIPWLLSPESLDIKEINGNKITCRGLVEYFKAYIKIYQGEELPHPKSMLQATAEANNLAAVATAKDTYNKKMEEICGGDKPFLAPNDLQTKHLQLKEESVKLFRGVKKMGGEEFSRRYLQQLESEIDELYIQYIKHNDSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2007
R free: 0.2369
Average B factor: 67.18
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293.15
Crystal growth procedure: 3.5 M sodium formate pH 7, crystals transferred to cryo solution supplemented with 25% glycerol
Matthews coefficient: 3.77
Solvent content (%): 67.39
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2021-06-30
Protein Tyrosine Phosphatase 1B Delta helix 7, P185G mutant, open state (PDB entry 5KAA)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 289 residues
Sequence: GHMASMEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVGESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.968
R work: 0.1728
R free: 0.2104
Average B factor: 25.843
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES, pH 8.0, 0.2 M MgCl2, 19% PEG8000
Matthews coefficient: 2.49
Solvent content (%): 50.64
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: 2017-03-08
Crystal structure of PAK1 in complex with an inhibitor compound G-5555 (PDB entry 5DEY)
Macromolecule: Serine/threonine-protein kinase PAK 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: SDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1834
R free: 0.2275
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: crystals were grown at 19  C from 1.0 uL + 1.0 uL vapor diffusion drops containing 10 mg/mL protein, 1 mM ligand, 0.15 M DL-Malic Acid pH 7.0, 20% - 30% PEG 3350, 4% 1,3-Propanediol and 0.1 M Sodium Malonate, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Matthews coefficient: 2.4
Solvent content (%): 48.69
Ligand: 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one (59T)
Ligand formula: C25 H25 Cl N6 O3
Ligand molecular weight: 492.957
Ligand SMILES: Cc1cccc(n1)c2ccc(c(c2)Cl)C3=Cc4cnc(nc4N(C3=O)CC5OCC(CO5)N)NC
Ligand InChI: InChI=1S/C25H25ClN6O3/c1-14-4-3-5-21(30-14)15-6-7-18(20(26)9-15)19-8-16-10-29-25(28-2)31-23(16)32(24(19)33)11-22-34-12-17(27)13-35-22/h3-10,17,22H,11-13,27H2,1-2H3,(H,28,29,31)/t17-,22-
Release date: 2016-01-27
CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone (PDB entry 5HNB)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 370 residues
Sequence: DDKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.21712
R free: 0.25243
Average B factor: 48.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 0.2M lithium chloride
Matthews coefficient: 3.08
Solvent content (%): 60.08
Ligand: [6-hydroxy-3-(3-methylbenzyl)-1H-indazol-5-yl][(3S)-3-hydroxypyrrolidin-1-yl]methanone (62M)
Ligand formula: C20 H21 N3 O3
Ligand molecular weight: 351.399
Ligand SMILES: Cc1cccc(c1)Cc2c3cc(c(cc3[nH]n2)O)C(=O)N4CCC(C4)O
Ligand InChI: InChI=1S/C20H21N3O3/c1-12-3-2-4-13(7-12)8-17-15-9-16(19(25)10-18(15)22-21-17)20(26)23-6-5-14(24)11-23/h2-4,7,9-10,14,24-25H,5-6,8,11H2,1H3,(H,21,22)/t14-/m0/s1
Release date: 2016-04-27
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOMB000242a (PDB entry 5QF9)
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): 1.94
R work: 0.2154
R free: 0.2664
Average B factor: 55.9559
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, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.41
Solvent content (%): 63.97
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: 2018-10-10