satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human DHODH in complex with inhibitor 1214 (PDB entry 6LP6)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 366 residues
Sequence: ATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.795
R work: 0.1545
R free: 0.178
Average B factor: 26.26
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: hepes pH4.6
2M AMMONIUM SULPHATE
30%Glycerol
Matthews coefficient: 3.67
Solvent content (%): 66.49
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2020-09-30
Introduction of a methyl group curbs metabolism of pyrido[3,4-d]pyrimidine MPS1 inhibitors and enables the discovery of the Phase 1 clinical candidate BOS172722. (PDB entry 6H3K)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 279 residues
Sequence: QSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.208
R free: 0.231
Average B factor: 103.23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M Bis-Tris propane; 
0.1 M MgCl2
0.1 M Sodium formate
18-26% PEG3350
Matthews coefficient: 3.43
Solvent content (%): 64.12
Ligand: ~{N}8-(2,2-dimethylpropyl)-~{N}2-[2-ethoxy-4-(4-methyl-1,2,4-triazol-3-yl)phenyl]-6-methyl-pyrido[3,4-d]pyrimidine-2,8-diamine (FMW)
Ligand formula: C24 H30 N8 O
Ligand molecular weight: 446.548
Ligand SMILES: CCOc1cc(ccc1Nc2ncc3cc(nc(c3n2)NCC(C)(C)C)C)c4nncn4C
Ligand InChI: InChI=1S/C24H30N8O/c1-7-33-19-11-16(22-31-27-14-32(22)6)8-9-18(19)29-23-25-12-17-10-15(2)28-21(20(17)30-23)26-13-24(3,4)5/h8-12,14H,7,13H2,1-6H3,(H,26,28)(H,25,29,30)
Release date: 2018-09-19
Crystal Structure of SETDB1 Tudor domain in complexed with (R,R)-59 (PDB entry 7CJT)
Macromolecule: Histone-lysine N-methyltransferase SETDB1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 240 residues
Sequence: GSSHHHHHHSSGENLYFQGGELSKDGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMKTSSASALE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.474
R work: 0.2043
R free: 0.2764
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.1%w/v n-Octyl-B-D-glucoside
0.1 M Sodium citrate trihydrate,pH 5.5
22% PEG3350
Matthews coefficient: 2.84
Solvent content (%): 56.7
Ligand: 2-[[(3~{R},5~{R})-1-methyl-5-(4-phenylmethoxyphenyl)piperidin-3-yl]amino]-3-prop-2-enyl-5~{H}-pyrrolo[3,2-d]pyrimidin-4-one (G09)
Ligand formula: C28 H31 N5 O2
Ligand molecular weight: 469.578
Ligand SMILES: CN1CC(CC(C1)NC2=Nc3cc[nH]c3C(=O)N2CC=C)c4ccc(cc4)OCc5ccccc5
Ligand InChI: InChI=1S/C28H31N5O2/c1-3-15-33-27(34)26-25(13-14-29-26)31-28(33)30-23-16-22(17-32(2)18-23)21-9-11-24(12-10-21)35-19-20-7-5-4-6-8-20/h3-14,22-23,29H,1,15-19H2,2H3,(H,30,31)/t22-,23+/m0/s1
Release date: 2021-04-14
Crystal structure of human tryptophan hydroxylase 1 in complex with inhibitor KM-05-080 (PDB entry 7ZIJ)
Macromolecule: Tryptophan 5-hydroxylase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.4
Sequence length: 326 residues
Sequence: MKHHHHHHHGAAGTSLYKKAGENLYFQGSVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94678362883
R work: 0.186253646429
R free: 0.225544799513
Average B factor: 35.6474442556
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 20% w/v PEG 5000 MME, 200 mM ammonium fluoride
Matthews coefficient: 2.37
Solvent content (%): 48.07
Ligand: 8-(1~{H}-benzimidazol-2-ylmethyl)-3-cyclopropyl-7-(phenylmethyl)purine-2,6-dione (IVW)
Ligand formula: C23 H20 N6 O2
Ligand molecular weight: 412.444
Ligand SMILES: c1ccc(cc1)Cn2c(nc3c2C(=O)NC(=O)N3C4CC4)Cc5[nH]c6ccccc6n5
Ligand InChI: InChI=1S/C23H20N6O2/c30-22-20-21(29(15-10-11-15)23(31)27-22)26-19(28(20)13-14-6-2-1-3-7-14)12-18-24-16-8-4-5-9-17(16)25-18/h1-9,15H,10-13H2,(H,24,25)(H,27,30,31)
Release date: 2022-09-07
Structure of Human KLK5 bound to anti-KLK5 Fab (PDB entry 7U5B)
Macromolecule: anti-KLK5 Fab Heavy Chain
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 224 residues
Sequence: EVQLVESGGGLVQPGGSLRLSCAASGFSLSSYGVTWVRQAPGKGLEWIGYITSNYGVSYYASWAKSRSTISRDTSKNTVYLQMGSLRAEDMAVYYCARENPDYGYAYDAWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.371
R work: 0.2216
R free: 0.2704
Average B factor: 75.722
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 15% PEG4K, 0.1 M MgSO4 and 0.1 M sodium citrate pH 5.0
Matthews coefficient: 3.04
Solvent content (%): 59.48
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: 2022-12-14
BTK1 SOAKED WITH COMPOUND 30 (PDB entry 7KXQ)
Macromolecule: Isoform BTK-C of Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 270 residues
Sequence: LGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.38
R work: 0.1507
R free: 0.1823
Average B factor: 17.132
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350
0.1 M Bis Tris Propane pH 7.5
0.2 M Sodium acetate trihydrate
Matthews coefficient: 2.28
Solvent content (%): 45.99
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: 2021-05-19
Crystal structure of uPA in complex with cleaved camostat (PDB entry 7DZD)
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): 2.0
R work: 0.192
R free: 0.231
Average B factor: 18.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 2.0M ammonium sulfate, 50mM sodium citrate pH 4.6, 5% PEG 400
Matthews coefficient: 2.14
Solvent content (%): 42.62
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: 2021-07-14
X-ray structure of protein kinase ck2 alpha subunit in D2O (PDB entry 5ZN1)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 329 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYAHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGAMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.05
R work: 0.16
R free: 0.18
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris-HCl, 1.2M ammonium sulfate, 5% acetonitrile, 2mM DTT
Matthews coefficient: 2
Solvent content (%): 38.58
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: 2018-11-21
Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103050 (PDB entry 5QIQ)
Macromolecule: Ubiquitin thioesterase OTUB2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 225 residues
Sequence: FNLISEKCDILSILRDHPENRIYRRKIEELSKRFTAIRKTKGDRNCFYRALGYSYLESLLGKSREIFKFKERVLQTPNDLLAAGFEEHKFRNFFNAFYSVVELVEKDGSVSSLLKVFNDQSASDHIVQFLRLLTSAFIRNRADFFRHFIDEEMDIKDFCTHEVEPMATECDHIQITALSQALSIALQVEYVDEMDTALNHHVFPEAATPSVYLLYKTSHYNILYA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.148
R free: 0.2008
Average B factor: 17.878
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT
Matthews coefficient: 2.39
Solvent content (%): 48.58
Ligand: DI(HYDROXYETHYL)ETHER (PEG)
Ligand formula: C4 H10 O3
Ligand molecular weight: 106.12
Ligand SMILES: C(COCCO)O
Ligand InChI: InChI=1S/C4H10O3/c5-1-3-7-4-2-6/h5-6H,1-4H2
Release date: 2019-12-18
Crystal structure of human ribonuclease P/MRP proteins Rpp20/Rpp25 (PDB entry 6CWX)
Macromolecule: Ribonuclease P protein subunit p20
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.26.5
Sequence length: 142 residues
Sequence: GHMAENREPRGAVEAELDPVEYTLRKRLPSRLPRRPNDIYVNMKTDFKAQLARCQKLLDGGARGQNACSEIYIHGLGLAINRAINIALQLQAGSFGSLQVAANTSTVELVDELEPETDTREPLTRIRNNSAIHIRVFRVTPK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2134
R free: 0.2322
Average B factor: 54.096
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 100 mM potassium formate, pH 7.5, 300 mM magnesium sulfate, 4.5% PEG 300, 4.5% PEG 400, 4.5% PEG 1000, 4.5% PEG 4000, and 4.5% PEG 8000
Matthews coefficient: 3.42
Solvent content (%): 63.93
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2018-04-18
STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 gene product) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR AR18 (PDB entry 6HMD)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 365 residues
Sequence: HMGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1
R work: 0.1493
R free: 0.1718
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 180 MICROLITER ENZYME STOCK SOLUTION (6 MG/ML IN 500 MM NACL, 25 MM TRIS/HCL, PH 8.5) WAS MIXED and incubated WITH 20 MIKROLITER of a STOCK SOLUTION of the inhibitor 4B0 (10 MM 4B0 IN DMSO). 20 MICROLITERS OF the resulting solution WAS MIXED WITH 10 MICROLITERS OF RESERVOIR SOLUTION (700 MM LICL, 28 % (W/V) PEG 6000, 100 MM TRIS/HCL, PH 8.5) IN EACH WELL OF A CRYSTALLIZATION PLATE. A SINGLE MACROSEED, grown UNDER THE SAME CONDITIONS, WAS ADDED TO EACH DROPLET of the plate. THE DROPLETS WERE EQUILIBRATED AT 293.15 K using the sitting drop variant of the VAPOR DIFFUSION method. This procedure generated large single crystals of a CK2alpha'/4B0 complex. Afterwards, the inhibitor 4B0 was exchanged against AR18 by an extensive soaking procedure of several steps.
Matthews coefficient: 2.24
Solvent content (%): 44.98
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: 2019-03-27
Crystal structure of CaMKII-actinin complex bound to ADP (PDB entry 7B57)
Macromolecule: Calcium/calmodulin-dependent protein kinase type II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.7.11.17
Sequence length: 317 residues
Sequence: SMMATITCTRFTEEYQLFEELGKGAFSVVRRCVKVLAGQEYAAKIINTKKLSARDHQKLEREARICRLLKHPNIVRLHDSISEEGHHYLIFDLVTGGELFEDIVAREYYSEADASHCIQQILEAVLHCHQMGVVHRDLKPENLLLASKLKGAAVKLADFGLAIEVEGEQQAWFGFAGTPGYLSPEVLRKDPYGKPVDLWACGVILYILLVGYPPFWDEDQHRLYQQIKAGAYDFPSPEWDTVTPEAKDLINKMLTINPSKRITAAEALKHPWISHRSTVASCMHRQETVDCLKKFNARRKLKGAILAAMLATRNFSG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2031
R free: 0.2474
Average B factor: 43.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M MES pH 6.0, 20% w/v PEG4000, 0.2 M Lithium Sulfate
Matthews coefficient: 2.48
Solvent content (%): 50.32
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2022-06-22
Crystal structure of the catalytic domain of human JARID1B in complex with MC3948 (PDB entry 5FZG)
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): 1.96
R work: 0.1868
R free: 0.2242
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: 2.09
Solvent content (%): 41.19
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: 2017-03-29
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000693a (PDB entry 5QGG)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.1901
R free: 0.2236
Average B factor: 36.771
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.29
Solvent content (%): 71.35
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2019-03-27
Crystal structure of TYK2 kinase domain in complex with compound 25 (PDB entry 7UYT)
Macromolecule: Non-receptor tyrosine-protein kinase TYK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: PTVFHKRYLKKIRDLGEGHFGKVSLYCYDPTNDGTGEMVAVKALKADCGPQHRSGWKQEIDILRTLYHEHIIKYKGCCEDQGEKSLQLVMEYVPLGSLRDYLPRHSIGLAQLLLFAQQICEGMAYLHAQHYIHRDLAARNVLLDNDRLVKIGDFGLAKAVPEGHEYYRVREDGDSPVFWYAPECLKEYKFYYASDVWSFGVTLYELLTHCDSSQSPPTKFLELIGIAQGQMTVLRLTELLERGERLPRPDKCPCEVYHLMKNCWETEASFRPTFENLIPILKTVHEKYQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.2392
R free: 0.2929
Average B factor: 46.775
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 291
Crystal growth procedure: Crystals of human TYK2 in complex with the ligand were prepared according to established protocols
Matthews coefficient: 2.15
Solvent content (%): 42.75
Ligand: 6-{[(2M)-2-(2-chloro-6-fluorophenyl)-5-oxo-5H-pyrrolo[3,4-b]pyridin-4-yl]amino}-N-ethylpyridine-3-carboxamide (OV5)
Ligand formula: C21 H15 Cl F N5 O2
Ligand molecular weight: 423.828
Ligand SMILES: CCNC(=O)c1ccc(nc1)Nc2cc(nc3c2C(=O)N=C3)c4c(cccc4Cl)F
Ligand InChI: InChI=1S/C21H15ClFN5O2/c1-2-24-20(29)11-6-7-17(25-9-11)28-15-8-14(18-12(22)4-3-5-13(18)23)27-16-10-26-21(30)19(15)16/h3-10H,2H2,1H3,(H,24,29)(H,25,27,28)
Release date: 2022-08-24
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001648a (PDB entry 5RB7)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.193
R free: 0.2168
Average B factor: 30.166
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.81
Solvent content (%): 56.24
Ligand: (1R,3S)-N-[(2H-1,3-benzodioxol-5-yl)methyl]-3-methylcyclopentan-1-amine (S4D)
Ligand formula: C14 H19 N O2
Ligand molecular weight: 233.306
Ligand SMILES: CC1CCC(C1)NCc2ccc3c(c2)OCO3
Ligand InChI: InChI=1S/C14H19NO2/c1-10-2-4-12(6-10)15-8-11-3-5-13-14(7-11)17-9-16-13/h3,5,7,10,12,15H,2,4,6,8-9H2,1H3
Release date: 2020-04-22
Crystal structure of human BRR2 in complex with T-3905516 (PDB entry 5URJ)
Macromolecule: U5 small nuclear ribonucleoprotein 200 kDa helicase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 1738 residues
Sequence: GGSDLDQGGEALAPRQVLDLEDLVFTQGSHFMANKRCQLPDGSFRRQRKGYEEVHVPALKPKPFGSEEQLLPVEKLPKYAQAGFEGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAPMRSLVQEMVGSFGKRLATYGITVAELTGDHQLCKEEISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHLLHDDRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNYEDVATFLRVDPAKGLFYFDNSFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGKTARAIRDMCLEKDTLGLFLREGSASTEVLRTEAEQCKNLELKDLLPYGFAIHHAGMTRVDRTLVEDLFADKHIQVLVSTATLAWGVNLPAHTVIIKGTQVYSPEKGRWTELGALDILQMLGRAGRPQYDTKGEGILITSHGELQYYLSLLNQQLPIESQMVSKLPDMLNAEIVLGNVQNAKDAVNWLGYAYLYIRMLRSPTLYGISHDDLKGDPLLDQRRLDLVHTAALMLDKNNLVKYDKKTGNFQVTELGRIASHYYITNDTVQTYNQLLKPTLSEIELFRVFSLSSEFKNITVREEEKLELQKLLERVPIPVKESIEEPSAKINVLLQAFISQLKLEGFALMADMVYVTQSAGRLMRAIFEIVLNRGWAQLTDKTLNLCKMIDKRMWQSMCPLRQFRKLPEEVVKKIEKKNFPFERLYDLNHNEIGELIRMPKMGKTIHKYVHLFPKLELSVHLQPITRSTLKVELTITPDFQWDEKVHGSSEAFWILVEDVDSEVILHHEYFLLKAKYAQDEHLITFFVPVFEPLPPQYFIRVVSDRWLSCETQLPVSFRHLILPEKYPPPTELLDLQPLPVSALRNSAFESLYQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQSSEGRCVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLKLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLIGGENGPVLEVICSRMRYISSQIERPIRIVALSSSLSNAKDVAHWLGCSATSTFNFHPNVRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTRLTAIDILTTCAADIQRQRFLHCTEKDLIPYLEKLSDSTLKETLLNGVGYLHEGLSPMERRLVEQLFSSGAIQVVVASRSLCWGMNVAAHLVIIMDTQYYNGKIHAYVDYPIYDVLQMVGHANRPLQDDEGRCVIMCQGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVTKTIENKQDAVDYLTWTFLYRRMTQNPNYYNLQGISHRHLSDHLSELVEQTLSDLEQSKCISIEDEMDVAPLNLGMIAAYYYINYTTIELFSMSLNAKTKVRGLIEIISNAAEYENIPIRHHEDNLLRQLAQKVPHKLNNPKFNDPHVKTNLLLQAHLSRMQLSAELQSDTEEILSKAIRLIQACVDVLSSNGWLSPALAAMELAQMVTQAMWSKDSYLKQLPHFTSEHIKRCTDKGVESVFDIMEMEDEERNALLQLTDSQIADVARFCNRYPNIELSYEVVDKDSIRSGGPVVVLVQLEREEEVTGPVIAPLFPQKREEGWWVVIGDAKSNSLISIKRLTLQQKAKVKLDFVAPATGAHNYTLYFMSDAYMGCDQEYKFSVDVKEA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.2373
R free: 0.2862
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.25-1.5M sodium malonate, 100mM sodium citrate pH 5.0-5.3, 10mg/ml BRR2
Matthews coefficient: 3.45
Solvent content (%): 64.33
Ligand: 6-benzyl-3-[(2R)-2-(3-fluoropyridin-2-yl)-6-methyl-3,4-dihydro-2H-1-benzopyran-7-yl]-4,6-dihydropyrido[4,3-d]pyrimidine-2,7(3H,8H)-dione (8LS)
Ligand formula: C29 H25 F N4 O3
Ligand molecular weight: 496.532
Ligand SMILES: Cc1cc2c(cc1N3CC4=CN(C(=O)CC4=NC3=O)Cc5ccccc5)OC(CC2)c6c(cccn6)F
Ligand InChI: InChI=1S/C29H25FN4O3/c1-18-12-20-9-10-25(28-22(30)8-5-11-31-28)37-26(20)14-24(18)34-17-21-16-33(15-19-6-3-2-4-7-19)27(35)13-23(21)32-29(34)36/h2-8,11-12,14,16,25H,9-10,13,15,17H2,1H3/t25-/m1/s1
Release date: 2017-07-19