satarupa22/MacromolecularLigandDB huggingface dataset:
X-ray structure of the adduct formed upon reaction of cisplatin with human angiogenin after 5 days soaking (PDB entry 8OO3)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 123 residues
Sequence: QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVHLDQSIFRRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.243
R free: 0.2905
Average B factor: 20.824
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.1
Crystallization temperature (K): 293
Crystal growth procedure: 10% PEG6K, 20 mM sodium citrate pH 5.1, 0.2 M sodium/potassium tartrate
Matthews coefficient: 2.16
Solvent content (%): 43.13
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: 2023-07-12
Crystal structure of CREBBP bromodomain complexed with DSPB2A002 (PDB entry 5OWK)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1621
R free: 0.1761
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M MES, pH6.5, 0.1 M MgCl2, 20% PEG6K, 10% EG
Matthews coefficient: 2.15
Solvent content (%): 42.73
Ligand: ethyl 4-chloranyl-1-methyl-6-oxidanylidene-pyridine-3-carboxylate (7MX)
Ligand formula: C9 H10 Cl N O3
Ligand molecular weight: 215.634
Ligand SMILES: CCOC(=O)C1=CN(C(=O)C=C1Cl)C
Ligand InChI: InChI=1S/C9H10ClNO3/c1-3-14-9(13)6-5-11(2)8(12)4-7(6)10/h4-5H,3H2,1-2H3
Release date: 2018-08-29
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z2856434762 (PDB entry 7FRH)
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): 1.84
R work: 0.1624
R free: 0.194
Average B factor: 37.483
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.3
Solvent content (%): 62.76
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: 2022-11-23
HIF Prolyl Hydroxylase 2 (PHD2/EGLN1) in complex with tert-butyl 6-(5-hydroxy-4-(1H-1,2,3-triazol-1-yl)-1H-pyrazol-1-yl)nicotinate (IOX4) (PDB entry 6ZBN)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 227 residues
Sequence: PNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.2052
R free: 0.2299
Average B factor: 74.1576
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 0.15M Potassium thiocyanate pH 7, 20.5% PEG 3350, Sitting Drop (300 nL), protein-to-well ratio, 2:1, 298K
Matthews coefficient: 2.41
Solvent content (%): 49
Ligand: ~{tert}-butyl 6-[5-oxidanyl-4-(1,2,3-triazol-1-yl)pyrazol-1-yl]pyridine-3-carboxylate (QEE)
Ligand formula: C15 H16 N6 O3
Ligand molecular weight: 328.326
Ligand SMILES: CC(C)(C)OC(=O)c1ccc(nc1)n2c(c(cn2)n3ccnn3)O
Ligand InChI: InChI=1S/C15H16N6O3/c1-15(2,3)24-14(23)10-4-5-12(16-8-10)21-13(22)11(9-18-21)20-7-6-17-19-20/h4-9,22H,1-3H3
Release date: 2021-04-07
The crystal structure of a mouse Fab fragment TL1 in complex with a human Glucose-6-phosphate isomerase peptide 293-307 (PDB entry 8BBH)
Macromolecule: Glucose-6-phosphate isomerase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.3.1.9
Sequence length: 19 residues
Sequence: XCFEQLLSGAHWMDQHFCA
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.619
R work: 0.1976
R free: 0.2291
Average B factor: 25.727
Crystallization method: EVAPORATION
Crystallization temperature (K): 300
Crystal growth procedure: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8,000
Matthews coefficient: 2.51
Solvent content (%): 51.01
Release date: 2022-12-21
Crystal structure of human GSK3B in complex with G5 (PDB entry 7U31)
Macromolecule: Glycogen synthase kinase-3 beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.26
Sequence length: 350 residues
Sequence: KVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.2423
R free: 0.2759
Average B factor: 63.599
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: PEG3350, Sodium Chloride, Hepes
Matthews coefficient: 3.95
Solvent content (%): 68.84
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: 2022-04-27
Structure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 56 (PDB entry 7A6X)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 130 residues
Sequence: HMGAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.1505
R free: 0.1985
Average B factor: 17.831
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5
Matthews coefficient: 1.78
Solvent content (%): 30.88
Ligand: (2S,9S,12R)-2-cyclohexyl-12-[2-(3,4-dimethoxyphenyl)ethyl]-24,27-dimethoxy-11,18,22-trioxa-4-azatetracyclo[21.2.2.113,17.04,9]octacosa-1(25),13(28),14,16,23,26-hexaene-3,10-dione (R3B)
Ligand formula: C42 H53 N O9
Ligand molecular weight: 715.872
Ligand SMILES: COc1ccc(cc1OC)CCC2c3cccc(c3)OCCCOc4c(cc(cc4OC)C(C(=O)N5CCCCC5C(=O)O2)C6CCCCC6)OC
Ligand InChI: InChI=1S/C42H53NO9/c1-46-35-20-18-28(24-36(35)47-2)17-19-34-30-14-10-15-32(25-30)50-22-11-23-51-40-37(48-3)26-31(27-38(40)49-4)39(29-12-6-5-7-13-29)41(44)43-21-9-8-16-33(43)42(45)52-34/h10,14-15,18,20,24-27,29,33-34,39H,5-9,11-13,16-17,19,21-23H2,1-4H3/t33-,34+,39-/m0/s1
Release date: 2021-03-17
Crystal structure of selective IRE1a inhibitor 29 at the enzyme active site (PDB entry 8UVL)
Macromolecule: Serine/threonine-protein kinase/endoribonuclease IRE1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 448 residues
Sequence: MHHHHHHGENLYFQGSSPSLEQDDGDEETSVVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAIELCAATLQEYVEQKDFAHLGLEPITLLQQTTSGLAHLHSLNIVHRNLKPHNILISMPNAHGKIKAMISDFGLCKKLAVGRHSFSRRSGVPGTEGWIAPEMLSEDCKENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQANILLGACSLDCLHPEKHEDVIARELIEKMIAMDPQKRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPLQTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYFTSRFPHLLAHTYRAMELCSHERLFQPYYFHEPPEPQPPVTPDALGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.1808
R free: 0.251
Average B factor: 75.76
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 89mM HEPES pH 7.5, 32% PEG 200, 3% 6-aminohexanoic acid, 100mM lithium chloride
Matthews coefficient: 2.84
Solvent content (%): 56.65
Ligand: 1-phenyl-N-(2,3,6-trifluoro-4-{[(3M)-3-(2-{[(3R,5R)-5-fluoropiperidin-3-yl]amino}pyrimidin-4-yl)pyridin-2-yl]oxy}phenyl)methanesulfonamide (XOE)
Ligand formula: C27 H24 F4 N6 O3 S
Ligand molecular weight: 588.576
Ligand SMILES: c1ccc(cc1)CS(=O)(=O)Nc2c(cc(c(c2F)F)Oc3c(cccn3)c4ccnc(n4)NC5CC(CNC5)F)F
Ligand InChI: InChI=1S/C27H24F4N6O3S/c28-17-11-18(14-32-13-17)35-27-34-10-8-21(36-27)19-7-4-9-33-26(19)40-22-12-20(29)25(24(31)23(22)30)37-41(38,39)15-16-5-2-1-3-6-16/h1-10,12,17-18,32,37H,11,13-15H2,(H,34,35,36)
Release date: 2024-05-29
Nek2 kinase bound to inhibitor 102 (PDB entry 6SGK)
Macromolecule: Serine/threonine-protein kinase Nek2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 279 residues
Sequence: MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1954
R free: 0.2227
Average B factor: 33.9
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris pH 8.5, 3% PEG 8000
Matthews coefficient: 2.77
Solvent content (%): 55.61
Ligand: 2-phenylazanyl-9~{H}-purine-6-carbonitrile (LCQ)
Ligand formula: C12 H8 N6
Ligand molecular weight: 236.232
Ligand SMILES: c1ccc(cc1)Nc2nc(c3c(n2)[nH]cn3)C#N
Ligand InChI: InChI=1S/C12H8N6/c13-6-9-10-11(15-7-14-10)18-12(17-9)16-8-4-2-1-3-5-8/h1-5,7H,(H2,14,15,16,17,18)
Release date: 2020-06-17
Bromodomain of CBP liganded with iCBP7 (PDB entry 8FXN)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 116 residues
Sequence: KKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1967
R free: 0.2425
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 0.03M Sodium nitrate, 0.03 Sodium phosphate dibasic, 0.03M Ammonium sulfate, 0.1 M Imidazole, 0.1 M MES pH 6.5, 20% v/v PEG 500 MME; 10% w/v PEG 20000
Matthews coefficient: 2.18
Solvent content (%): 43.58
Ligand: tert-butyl {(1R,4s)-4-[(5M)-2-[(2S)-1-(3-tert-butylphenyl)-6-oxopiperidin-2-yl]-5-(3,5-dimethyl-1,2-oxazol-4-yl)-1H-benzimidazol-1-yl]cyclohexyl}carbamate (YN0)
Ligand formula: C38 H49 N5 O4
Ligand molecular weight: 639.827
Ligand SMILES: Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCC(CC4)NC(=O)OC(C)(C)C)C5CCCC(=O)N5c6cccc(c6)C(C)(C)C
Ligand InChI: InChI=1S/C38H49N5O4/c1-23-34(24(2)47-41-23)25-15-20-31-30(21-25)40-35(43(31)28-18-16-27(17-19-28)39-36(45)46-38(6,7)8)32-13-10-14-33(44)42(32)29-12-9-11-26(22-29)37(3,4)5/h9,11-12,15,20-22,27-28,32H,10,13-14,16-19H2,1-8H3,(H,39,45)/t27-,28+,32-/m0/s1
Release date: 2024-02-07
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z321318226 (PDB entry 7FRI)
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): 1.86
R work: 0.1608
R free: 0.1949
Average B factor: 40.817
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.3
Solvent content (%): 62.72
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: 2022-11-23
Crystal structure of the catalytic domain of MMP-13 complexed with 4-oxo-N-(3-(2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy)benzyl)-3,4-dihydroquinazoline-2-carboxamide (PDB entry 5B5P)
Macromolecule: Collagenase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24
Sequence length: 172 residues
Sequence: EYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDPN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1733
R free: 0.208
Average B factor: 24.4984
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100mM TrisHCl, 1000mM ammonium formate, 15.3% PEG8000
Matthews coefficient: 2.36
Solvent content (%): 47.86
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: 2017-01-18
Notum ARUK3003710 (PDB entry 7BNL)
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): 1.23
R work: 0.178
R free: 0.1978
Average B factor: 28.6284
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: 1.93
Solvent content (%): 36.13
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: 2022-03-02
Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 7i (PDB entry 5NRF)
Macromolecule: Chitotriosidase-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.14
Sequence length: 377 residues
Sequence: AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEESGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQELSLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.447
R work: 0.144
R free: 0.1693
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 290
Crystal growth procedure: 25% (w/v) polyethylene glycol (PEG) 3350, 200 mM potassium sodium tartrate (PST) at pH 7.2
Matthews coefficient: 2.27
Solvent content (%): 45.82
Ligand: 1-(3-azanyl-1~{H}-1,2,4-triazol-5-yl)-~{N}-[2-(4-chlorophenyl)ethyl]-~{N}-(phenylmethyl)piperidin-4-amine (95Q)
Ligand formula: C22 H27 Cl N6
Ligand molecular weight: 410.943
Ligand SMILES: c1ccc(cc1)CN(CCc2ccc(cc2)Cl)C3CCN(CC3)c4[nH]nc(n4)N
Ligand InChI: InChI=1S/C22H27ClN6/c23-19-8-6-17(7-9-19)10-13-29(16-18-4-2-1-3-5-18)20-11-14-28(15-12-20)22-25-21(24)26-27-22/h1-9,20H,10-16H2,(H3,24,25,26,27)
Release date: 2018-03-28
Human cationic trypsin (TRY1) complexed with serine protease inhibitor Kazal type 1 (SPINK1) (PDB entry 7QE8)
Macromolecule: Trypsin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.4
Sequence length: 224 residues
Sequence: IVGGYNCEENSVPYQVSLNSGYHFCGGSLINEQWVVSAGHCYKSRIQVRLGEHNIEVLEGNEQFINAAKIIRHPQYDRKTLNNDIMLIKLSSRAVINARVSTISLPTAPPATGTKCLISGWGNTASSGADYPDELQCLDAPVLSQAKCEASYPGKITSNMFCVGFLEGGKDSCQGDAGGPVVCNGQLQGVVSWGDGCAQKNKPGVYTKVYNYVKWIKNTIAANS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2229
R free: 0.2431
Average B factor: 100.14
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 1 ul protein solution (20 mg/mL in 20 mM HEPES, pH 7.4, 150 mM NaCl) + 1 ul well solution (15% PEG 4000, 0.3 M AS), cryo 15% PEG 4000, 0.3 M AS, 8% PEG 400
Matthews coefficient: 2.7
Solvent content (%): 54
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: 2022-03-30
A fragment-based inhibitor of SHP2 (PDB entry 8S01)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 537 residues
Sequence: HMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.18028
R free: 0.23148
Average B factor: 54.533
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.5M K formate
15% PEG 3350
0.1M pH=8 Bis-Tris propane/HCl
Matthews coefficient: 2.27
Solvent content (%): 45.77
Ligand: 3-(4-chlorophenyl)-1H-pyrazole (A1H4J)
Ligand formula: C9 H7 Cl N2
Ligand molecular weight: 178.618
Ligand SMILES: c1cc(ccc1c2cc[nH]n2)Cl
Ligand InChI: InChI=1S/C9H7ClN2/c10-8-3-1-7(2-4-8)9-5-6-11-12-9/h1-6H,(H,11,12)
Release date: 2024-03-20
Crystal structure of the human dihydroorotase domain in complex with the anticancer drug 5-fluorouracil (PDB entry 8GVZ)
Macromolecule: CAD protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.2.3
Sequence length: 391 residues
Sequence: MTSQKLVRLPGLIDVHVHLREPGGTHKEDFASGTAAALAGGITMVCAMPNTRPPIIDAPALALAQKLAEAGARCDFALFLGASSENAGTLGTVAGSAAGLKLYLNETFSELRLDSVVQWMEHFETWPSHLPIVAHAEQQTVAAVLMVAQLTQRSVHICHVARKEEILLIKAAKARGLPVTCEVAPHHLFLSHDDLERLGPGKGEVRPELGSRQDVEALWENMAVIDCFASDHAPHTLEEKCGSRPPPGFPGLETMLPLLLTAVSEGRLSLDDLLQRLHHNPRRIFHLPPQEDTYVEVDLEHEWTIPSHMPFSKAHWTPFEGQKVKGTVRRVVLRGEVAYIDGQVLVPPGYGQDVRKWPQGAVPQLPPSAPATSEMTTTPERPRRGIPGLPD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.1774
R free: 0.2148
Average B factor: 25.3689
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M MES, pH 6.5, 1.6M potassium sodium tartrate tetrahydrate
Matthews coefficient: 2.51
Solvent content (%): 51.04
Ligand: 5-FLUOROURACIL (URF)
Ligand formula: C4 H3 F N2 O2
Ligand molecular weight: 130.077
Ligand SMILES: C1=C(C(=O)NC(=O)N1)F
Ligand InChI: InChI=1S/C4H3FN2O2/c5-2-1-6-4(9)7-3(2)8/h1H,(H2,6,7,8,9)
Release date: 2023-09-20
Crystal structure of uPA in complex with nafamostat (PDB entry 7VM4)
Macromolecule: Urokinase-type plasminogen activator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 245 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.175
R free: 0.224
Average B factor: 25.5
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2.0 M ammonium sulfate, 5% PEG400, 20 mM sodium citrate, pH 4.6
Matthews coefficient: 2.15
Solvent content (%): 42.84
Ligand: 4-carbamimidamidobenzoic acid (GBS)
Ligand formula: C8 H9 N3 O2
Ligand molecular weight: 179.176
Ligand SMILES: c1cc(ccc1C(=O)O)NC(=N)N
Ligand InChI: InChI=1S/C8H9N3O2/c9-8(10)11-6-3-1-5(2-4-6)7(12)13/h1-4H,(H,12,13)(H4,9,10,11)
Release date: 2022-10-12
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000688a (PDB entry 7GTP)
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): 2.47
R work: 0.1958
R free: 0.2522
Average B factor: 43.694
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: 3.36
Solvent content (%): 63.42
Ligand: (4-acetylphenoxy)acetic acid (W1D)
Ligand formula: C10 H10 O4
Ligand molecular weight: 194.184
Ligand SMILES: CC(=O)c1ccc(cc1)OCC(=O)O
Ligand InChI: InChI=1S/C10H10O4/c1-7(11)8-2-4-9(5-3-8)14-6-10(12)13/h2-5H,6H2,1H3,(H,12,13)
Release date: 2024-01-24