satarupa22/MacromolecularLigandDB huggingface dataset:
Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 4 (PDB entry 5C3K)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 110 residues
Sequence: GSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.02
R work: 0.21696
R free: 0.25995
Average B factor: 41.124
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Hepes-NaOH 7.5, 3.9M NaCl
Matthews coefficient: 2.32
Solvent content (%): 47
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: 2015-08-12
Human PDK1-PKCiota Kinase Chimera in Complex with Allosteric Compound PS267 Bound to the PIF-Pocket (PDB entry 5MRD)
Macromolecule: 3-phosphoinositide-dependent protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 310 residues
Sequence: AMDGTAAEPRPGAGSLQHAQPPPQPRSKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKIVEKRHVNKENKIPYVQREKDVMSRLDHPFFVKLYFCFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANSFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.41
R work: 0.1402
R free: 0.1742
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, 10 MM DTT
Matthews coefficient: 2.17
Solvent content (%): 43.27
Ligand: ethyl
(2~{S})-1-(6-chloranyl-1,3-benzothiazol-2-yl)-4-oxidanyl-5-oxidanylidene-2-thiophen-2-yl-2~{H}-pyrrole-3-carboxylate (S26)
Ligand formula: C18 H13 Cl N2 O4 S2
Ligand molecular weight: 420.89
Ligand SMILES: CCOC(=O)C1=C(C(=O)N(C1c2cccs2)c3nc4ccc(cc4s3)Cl)O
Ligand InChI: InChI=1S/C18H13ClN2O4S2/c1-2-25-17(24)13-14(11-4-3-7-26-11)21(16(23)15(13)22)18-20-10-6-5-9(19)8-12(10)27-18/h3-8,14,22H,2H2,1H3/t14-/m1/s1
Release date: 2017-01-18
Crystal structure of human choline alpha in complex with an inhibitor (PDB entry 7NB3)
Macromolecule: Choline kinase alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.32
Sequence length: 384 residues
Sequence: GPQPPADEQPEPRTRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYGAILQMRSCNKEGSEQAQKENEFQGAEAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1893
R free: 0.2342
Average B factor: 40.519
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 18-20% Peg-mme 5000, 0.1 M Magnesium Formate, 0.1 M HEPES pH 7.0
Matthews coefficient: 2.45
Solvent content (%): 49.78
Ligand: 4-(6-azanyl-2-pyridin-4-yl-purin-9-yl)-~{N}-(3-methoxyphenyl)cyclohexane-1-carboxamide (U6H)
Ligand formula: C24 H25 N7 O2
Ligand molecular weight: 443.501
Ligand SMILES: COc1cccc(c1)NC(=O)C2CCC(CC2)n3cnc4c3nc(nc4N)c5ccncc5
Ligand InChI: InChI=1S/C24H25N7O2/c1-33-19-4-2-3-17(13-19)28-24(32)16-5-7-18(8-6-16)31-14-27-20-21(25)29-22(30-23(20)31)15-9-11-26-12-10-15/h2-4,9-14,16,18H,5-8H2,1H3,(H,28,32)(H2,25,29,30)/t16-,18+
Release date: 2021-10-13
Crystal structure of 1-hydroxy-4-(trifluoromethyl)pyridine-2(1H)-thione bound to human carbonic anhydrase II (PDB entry 4Q87)
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): 1.55
R work: 0.1691
R free: 0.20561
Average B factor: 9.077
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium Sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.09
Solvent content (%): 41.22
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: 2015-03-11
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment N05859b (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) (PDB entry 5FZ6)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.1786
R free: 0.2186
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.17
Solvent content (%): 43.38
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: 2016-03-23
DDR1, 3-chloro-N-[4-chloro-3-(1H-pyrrolo[2,3-b]pyridin-5-ylcarbamoyl)phenyl]-4-(2-hydroxyethylamino)benzamide, 1.802A, P212121, Rfree=22.2% (PDB entry 5SAZ)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1874
R free: 0.2244
Average B factor: 36.074
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7.6 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed with reservoir consisting of 0.1M MES/NaOH pH 6.5, 0.2M KI, 25% PEG 4000
Matthews coefficient: 2.4
Solvent content (%): 48.78
Ligand: 2-chloro-5-{3-chloro-4-[(2-hydroxyethyl)amino]benzamido}-N-(1H-pyrrolo[2,3-b]pyridin-5-yl)benzamide (1IW)
Ligand formula: C23 H19 Cl2 N5 O3
Ligand molecular weight: 484.335
Ligand SMILES: c1cc(c(cc1C(=O)Nc2ccc(c(c2)C(=O)Nc3cc4cc[nH]c4nc3)Cl)Cl)NCCO
Ligand InChI: InChI=1S/C23H19Cl2N5O3/c24-18-3-2-15(29-22(32)14-1-4-20(19(25)10-14)26-7-8-31)11-17(18)23(33)30-16-9-13-5-6-27-21(13)28-12-16/h1-6,9-12,26,31H,7-8H2,(H,27,28)(H,29,32)(H,30,33)
Release date: 2022-06-29
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B52 (PDB entry 7THD)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 163 residues
Sequence: NPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.16
R work: 0.1357
R free: 0.1516
Average B factor: 12.43
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 15% PEG 3350
0.5 M KH2PO4
1 mM NaCl
Protein and inhibitor were mixed in ratio 1:2
1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor
Matthews coefficient: 2.39
Solvent content (%): 48.6
Ligand: [(4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}[1,1'-biphenyl]-4-yl)methyl]propanedioic acid (I4V)
Ligand formula: C53 H61 N7 O11
Ligand molecular weight: 972.092
Ligand SMILES: c1ccc(cc1)CC23CCCN(C2)C(=O)C=CC(=O)NCCC(NC(=O)Cc4ccccc4CNC(=O)C(NC3=O)Cc5ccc(cc5)c6ccc(cc6)CC(C(=O)O)C(=O)O)C(=O)NCCOCCN
Ligand InChI: InChI=1S/C53H61N7O11/c54-23-27-71-28-25-56-48(64)43-21-24-55-45(61)19-20-47(63)60-26-6-22-53(34-60,32-37-7-2-1-3-8-37)52(70)59-44(49(65)57-33-41-10-5-4-9-40(41)31-46(62)58-43)30-36-13-17-39(18-14-36)38-15-11-35(12-16-38)29-42(50(66)67)51(68)69/h1-5,7-20,42-44H,6,21-34,54H2,(H,55,61)(H,56,64)(H,57,65)(H,58,62)(H,59,70)(H,66,67)(H,68,69)/b20-19+/t43-,44-,53-/m0/s1
Release date: 2022-08-24
Carbonic Anhydrase II complexed with ureic benzene sulfonamide MB9-561B (PDB entry 6OTO)
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): 1.496
R work: 0.1711
R free: 0.191
Average B factor: 22.9427
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris Hal, pH7.8
Matthews coefficient: 2.04
Solvent content (%): 39.82
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: 2020-05-06
Crystal structure of DNMT3a ADD domain bound to H3 peptide (PDB entry 4QBQ)
Macromolecule: DNA (cytosine-5)-methyltransferase 3A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 137 residues
Sequence: GPLGSLVYEVRQKCRNIEDICISCGSLNVTLEHPLFVGGMCQNCKNCFLECAYQYDDDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRREDWPSRLQMFFA
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.406
R work: 0.1736
R free: 0.2304
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 29% PEGMME5000, 0.1M Bis-Tris Propane-HCL, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 2.12
Solvent content (%): 41.95
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: 2015-05-13
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with Z509756472 (PDB entry 7FRM)
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): 1.91
R work: 0.1597
R free: 0.1915
Average B factor: 39.993
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 (%): 62.73
Ligand: N-[(4-cyanophenyl)methyl]morpholine-4-carboxamide (JGG)
Ligand formula: C13 H15 N3 O2
Ligand molecular weight: 245.277
Ligand SMILES: c1cc(ccc1CNC(=O)N2CCOCC2)C#N
Ligand InChI: InChI=1S/C13H15N3O2/c14-9-11-1-3-12(4-2-11)10-15-13(17)16-5-7-18-8-6-16/h1-4H,5-8,10H2,(H,15,17)
Release date: 2022-11-23
TAS-120 covalent complex with FGFR1 (PDB entry 6MZW)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GAMSGVSEYELPEDPRWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.24099
R free: 0.29695
Average B factor: 49.226
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: MPEG 5000, ammonium sulfate, sodium cacodylate
Matthews coefficient: 2.26
Solvent content (%): 45.59
Ligand: 1-[(3S)-3-{4-amino-3-[(3,5-dimethoxyphenyl)ethynyl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}pyrrolidin-1-yl]prop-2-en-1-one (TZ0)
Ligand formula: C22 H22 N6 O3
Ligand molecular weight: 418.448
Ligand SMILES: COc1cc(cc(c1)OC)C#Cc2c3c(ncnc3n(n2)C4CCN(C4)C(=O)C=C)N
Ligand InChI: InChI=1S/C22H22N6O3/c1-4-19(29)27-8-7-15(12-27)28-22-20(21(23)24-13-25-22)18(26-28)6-5-14-9-16(30-2)11-17(10-14)31-3/h4,9-11,13,15H,1,7-8,12H2,2-3H3,(H2,23,24,25)/t15-/m0/s1
Release date: 2019-01-16
Crystal Structure of the UbArk2C fusion protein (PDB entry 7R70)
Macromolecule: Ubiquitin,E3 ubiquitin-protein ligase RNF165
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 183 residues
Sequence: GPLGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGGESGSGGSGSGAVQNTIERFTFPHKYKKRRPQDGKGKKDEGEESDTDEKCTICLSMLEDGEDVRRLPCMHLFHQLCVDQWLAMSKKCPICRVDIETQLGADS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.499
R work: 0.1997
R free: 0.2446
Average B factor: 72.3875
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 289.15
Crystal growth procedure: 1.6 M tri-sodium citrate
Matthews coefficient: 3.46
Solvent content (%): 64.52
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: 2022-03-09
syk in complex with compound 30 (PDB entry 6SSB)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 299 residues
Sequence: MDTEVYESPYADPEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.08
R work: 0.197
R free: 0.225
Average B factor: 50.22
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Na3Cit pH 6.4, 16% PEG3350, 0.2M KH2PO4
Matthews coefficient: 2.48
Solvent content (%): 50.35
Ligand: ~{N}-[4-[5-[(dimethylamino)methyl]-1-methyl-pyrazol-3-yl]pyrimidin-2-yl]-3-methyl-1-(5-methyl-1,3,4-oxadiazol-2-yl)imidazo[1,5-a]pyridin-7-amine (LUE)
Ligand formula: C22 H24 N10 O
Ligand molecular weight: 444.492
Ligand SMILES: Cc1nc(c2n1ccc(c2)Nc3nccc(n3)c4cc(n(n4)C)CN(C)C)c5nnc(o5)C
Ligand InChI: InChI=1S/C22H24N10O/c1-13-24-20(21-28-27-14(2)33-21)19-10-15(7-9-32(13)19)25-22-23-8-6-17(26-22)18-11-16(12-30(3)4)31(5)29-18/h6-11H,12H2,1-5H3,(H,23,25,26)
Release date: 2020-09-30
Crystal structure of PPARgamma with compound BR102375K (PDB entry 6ICJ)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 272 residues
Sequence: PESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.483
R work: 0.23
R free: 0.282
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M NH4 Acetate, 0.1 M HEPES 7.5 pH, 25 %w/v PEG 3350
Matthews coefficient: 2.27
Solvent content (%): 45.85
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: 2019-09-11
Discovery of VX-509 (Decernotinib): A Potent and Selective Janus kinase (JAK) 3 Inhibitor for the Treatment of Autoimmune Diseases (PDB entry 4YTH)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 296 residues
Sequence: GSHNMTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.1837
R free: 0.2152
Average B factor: 33.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.7-2.1 DL -malic acid pH 7.0, 2mM DTT
Matthews coefficient: 2.35
Solvent content (%): 47.72
Ligand: N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-2-methyl-N-(2,2,2-trifluoroethyl)-D-alaninamide (467)
Ligand formula: C17 H15 Cl F4 N6 O
Ligand molecular weight: 430.787
Ligand SMILES: CC(C)(C(=O)NCC(F)(F)F)Nc1c(cnc(n1)c2c[nH]c3c2cc(cn3)Cl)F
Ligand InChI: InChI=1S/C17H15ClF4N6O/c1-16(2,15(29)26-7-17(20,21)22)28-14-11(19)6-25-13(27-14)10-5-24-12-9(10)3-8(18)4-23-12/h3-6H,7H2,1-2H3,(H,23,24)(H,26,29)(H,25,27,28)
Release date: 2015-08-12
Crystal structure of the Pri1 subunit of human primase bound to ATP (PDB entry 6R4S)
Macromolecule: DNA primase small subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7
Sequence length: 410 residues
Sequence: GTSMETFDPTELPELLKLYYRRLFPYSQYYRWLNYGGVIKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEMQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICPKCWTLMTMAIRIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSLVKGGQDVKKKVHLSEKIHPFIRKSINIIKKYFEEYALVNQDILENKESWDKILALVPETIHDELQQSFQKSHNSLQRWEHLKKVASRYQNNIKNDKYGPWLEWEIMLQYCFPRLDINVSKGINHLLKSPFSVHPKTGRISVPIDLQKVDQFDPFTVPTISFICRELDAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDKSRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2275
R free: 0.2686
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 23% PEG3350, 10% ethylene glycol, 200 mM Na/K tartrate
Matthews coefficient: 2.51
Solvent content (%): 50.91
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: 2019-09-11
Fragment-based discovery of a highly potent, orally bioavailable inhibitor which modulates the phosphorylation and catalytic activity of ERK1/2 (PDB entry 6G8X)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 368 residues
Sequence: MAHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.165
R free: 0.217
Average B factor: 28.125
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.2
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES/NaOHpH=7.2, 34.0%w/v MPEG 2000, 0.02M Mercaptoethanol, 0.2M (NH4)2SO4
Matthews coefficient: 2.32
Solvent content (%): 46.87
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: 2018-05-30
Three dimensional structure of human carbonic anhydrase IX in complex with 5-(1-(4-Methoxyphenyl)-1H-1,2,3-triazol-4-yl)thiophene-2- sulfonamide (PDB entry 5FL5)
Macromolecule: CARBONIC ANHYDRASE IX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: GPDQSHWRYGGDPPWPRVSPACAGRFQSPVDIRPQLAAFSPALRPLELLGFQLPPLPELRLRNNGHSVQLTLPPGLEMALGPGREYRALQLHLHWGAAGRPGSEHTVEGHRFPAEIHVVHLSTAFARVDEALGRPGGLAVLAAFLEEGPEENSAYEQLLSRLEEIAEEGSETQVPGLDISALLPSDFSRYFQYEGSLTTPPCAQGVIWTVFNQTVMLSAKQLHTLSDTLWGPGDSRLQLNFRATQPLNGRVIEASFP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.15788
R free: 0.19563
Average B factor: 26.4
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 0.2 M LITHIUM SULFATE, 1.26 M AMMONIUM SULFATE, TRIS- HCL, PH 8.5, PROTEIN 10 MG/ML, 5-10 MM INHIBITOR(STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE) VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Matthews coefficient: 3.39
Solvent content (%): 63.69
Ligand: 5-[1-(4-methoxyphenyl)-1,2,3-triazol-4-yl]thiophene-2-sulfonamide (82E)
Ligand formula: C13 H12 N4 O3 S2
Ligand molecular weight: 336.389
Ligand SMILES: COc1ccc(cc1)n2cc(nn2)c3ccc(s3)S(=O)(=O)N
Ligand InChI: InChI=1S/C13H12N4O3S2/c1-20-10-4-2-9(3-5-10)17-8-11(15-16-17)12-6-7-13(21-12)22(14,18)19/h2-8H,1H3,(H2,14,18,19)
Release date: 2015-11-11