satarupa22/MacromolecularLigandDB huggingface dataset:
The co-crystal structure of DYRK2 with a small molecule inhibitor 6 (PDB entry 7DG4)
Macromolecule: Dual specificity tyrosine-phosphorylation-regulated kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 324 residues
Sequence: HDHVAYRYEVLKVIGKGSFGQVVKAYDHKVHQHVALKMVRNEKRFHRQAAEEIRILEHLRKQDKDNTMNVIHMLENFTFRNHICMTFELLSMNLYELIKKNKFQGFSLPLVRKFAHSILQCLDALHKNRIIHCDLKPENILLKQQGRSGIKVIDFGSSCYEHQRVYTYIQSRFYRAPEVILGARYGMPIDMWSLGCILAELLTGYPLLPGEDEGDQLACMIELLGMPSQKLLDASKRAKNFVSSKGYPRYCTVTTLSDGSVVLNGGRSRRGKLRGPPESREWGNALKGCDDPLFLDFLKQCLEWDPAVRMTPGQALRHPWLRRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.58
R work: 0.2013
R free: 0.2495
Average B factor: 65.3031
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.36M-0.5M sodium citrate tribasic dehydrate, 0.01M sodium borate, pH 7.5-9.5
Matthews coefficient: 3.65
Solvent content (%): 66.29
Ligand: 2,7-dimethoxy-9-(piperidin-4-ylmethylsulfanyl)acridine (H5R)
Ligand formula: C21 H24 N2 O2 S
Ligand molecular weight: 368.492
Ligand SMILES: COc1ccc2c(c1)c(c3cc(ccc3n2)OC)SCC4CCNCC4
Ligand InChI: InChI=1S/C21H24N2O2S/c1-24-15-3-5-19-17(11-15)21(26-13-14-7-9-22-10-8-14)18-12-16(25-2)4-6-20(18)23-19/h3-6,11-12,14,22H,7-10,13H2,1-2H3
Release date: 2021-11-10
Crystal structure of an engineered Botulinum Neurotoxin type B mutant E1191M/S1199Y in complex with human synaptotagmin 2 (PDB entry 6G5G)
Macromolecule: Botulinum neurotoxin type B
Type: Protein, polypeptide(L)
Source organism: Clostridium botulinum
EC number: 3.4.24.69
Sequence length: 1291 residues
Sequence: MPVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHQLIYVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQAYEEISKEHLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEMKLFLAPIYDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.18962
R free: 0.22339
Average B factor: 44.844
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 294
Crystal growth procedure: 0.2 M magnesium chloride, Tris pH 7.0, 10% w/v PEG 8000
Matthews coefficient: 3.5
Solvent content (%): 65.1
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: 2019-01-16
Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of rhinovirus-14 (HRV14) (PDB entry 6HLT)
Macromolecule: Golgi resident protein GCP60
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 166 residues
Sequence: MESLPVIAAPSMWTRPQIKDFKEKIQQDADSVITVGRGEVVTVRVPTHEEGSYLFWEFATDNYDIGFGVYFEWTDSPNTAVSVHVSESSDDDEEEEENIGCEEKAKKNANKPLLDEIVPVYRRDCHEEVYAGSHQYPGRGVYLLKFDNSYSLWRSKSVYYRVYYTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.815
R work: 0.2104
R free: 0.2394
Average B factor: 55.2
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5
Matthews coefficient: 2.69
Solvent content (%): 54.31
Release date: 2019-07-24
Crystal structure of human LTA4H mutant R563A in open conformation (PDB entry 5NIE)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 617 residues
Sequence: MHHHHHHPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGAMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.603
R work: 0.2351
R free: 0.2909
Average B factor: 56.83
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 294
Crystal growth procedure: 20% (w/v) PEG MME 5000, 100 mM MES monohydrate pH 6.0, 150 mM Ammonium Sulfate
Matthews coefficient: 2.69
Solvent content (%): 54.3
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: 2017-08-23
KRAS full length wild-type in complex with RGL1 Ras association domain (PDB entry 7SCW)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 190 residues
Sequence: GSMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.156
R free: 0.1921
Average B factor: 29.75
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.05M Magnesium acetate tetrahydrate, 0.1M MES (pH 6.5), 26% v/v PEG 400
Matthews coefficient: 2.46
Solvent content (%): 50.07
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: 2022-05-18
Tankyrase-2 in complex with compound 52 (PDB entry 5ZQQ)
Macromolecule: Tankyrase-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 168 residues
Sequence: NTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.29
R work: 0.163
R free: 0.224
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M Tris pH 8.5, 2.4M (NH4)2HPO4
Matthews coefficient: 2.69
Solvent content (%): 54.36
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: 2019-04-03
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000733a (PDB entry 5QEA)
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): 1.743
R work: 0.1852
R free: 0.2182
Average B factor: 42.4398
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: 3.34
Solvent content (%): 63.15
Ligand: N-[(4-phenyloxan-4-yl)methyl]acetamide (JHS)
Ligand formula: C14 H19 N O2
Ligand molecular weight: 233.306
Ligand SMILES: CC(=O)NCC1(CCOCC1)c2ccccc2
Ligand InChI: InChI=1S/C14H19NO2/c1-12(16)15-11-14(7-9-17-10-8-14)13-5-3-2-4-6-13/h2-6H,7-11H2,1H3,(H,15,16)
Release date: 2018-10-10
Crystal structure of haspin in complex with tubercidin (PDB entry 6G38)
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: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.14326
R free: 0.16544
Average B factor: 22.281
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 51-63% MPD and 0.1M SPG buffer, pH 6.0-6.5
Matthews coefficient: 3.04
Solvent content (%): 59.54
Ligand: '2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL (TBN)
Ligand formula: C11 H14 N4 O4
Ligand molecular weight: 266.253
Ligand SMILES: c1cn(c2c1c(ncn2)N)C3C(C(C(O3)CO)O)O
Ligand InChI: InChI=1S/C11H14N4O4/c12-9-5-1-2-15(10(5)14-4-13-9)11-8(18)7(17)6(3-16)19-11/h1-2,4,6-8,11,16-18H,3H2,(H2,12,13,14)/t6-,7-,8-,11-/m1/s1
Release date: 2018-04-18
Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Cytosine and Incoming Ca-8oxodGTP (PDB entry 6AK9)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.91
R work: 0.16512
R free: 0.20361
Average B factor: 21.043
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES pH 7.5, 18% PEG 4000
Matthews coefficient: 2.51
Solvent content (%): 51.05
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2019-05-29
Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation (PDB entry 7APJ)
Macromolecule: RAC-alpha serine/threonine-protein kinase,Non-specific serine/threonine protein kinase,RAC-alpha serine/threonine-protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 440 residues
Sequence: ARMNDVAIVKEGWLHKRGEYIKTWRPRYFLLKNDGTFIGYKERPQDVDQREAPLNNFSVAQCQLMKTERPRPNTFIIRCLQWTTVIERTFHVETPEEREEWTTAIQTVADGLKKQEEEEMDASAEHTDMEVSLAKPKHRVTMNEFEYLKLLGKGTFGKVILVKEKATGRYYAMKILKKEVIVAKDEVAHTLTENRVLQNSRHPFLTALKYSFQTHDRLCFVMEYANGGELFFHLSRERVFSEDRARFYGAEIVSALDYLHSEKNVVYRDLKLENLMLDKDGHIKITDFGLCKEGIKDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILMEEIRFPRTLGPEAKSLLSGLLKKDPKQRLGGGSEDAKEIMQHRFFAGIVWQHVYEKKLSPPFKPQVTSETDTRYFDEEFTAQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.211
R free: 0.2519
Average B factor: 58.66
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 295
Crystal growth procedure: 200 mM malonate, pH 5.0, 16% PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.3
Release date: 2021-08-25
Crystal structure of the ERp44-peroxiredoxin 4 complex (PDB entry 5HQP)
Macromolecule: Peroxiredoxin-4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.11.1.15
Sequence length: 246 residues
Sequence: MRGSHHHHHHGSWETEERPRTREEESHFYAGGQVYPGEASRVSVADHSLHLSKAKISKPAPYWEGTAVIDGEFKELKLTDYRGKYLVFFFYPLDFTFVSPTEIIAFGDRLEEFRSINTEVVACSVDSQFEHLAWINTPRRQGGLGPIRIPLLSDLTHQISKDYGVYLEDSGHTLRGLFIIDDKGILRQITLNDLPVGRSVDETLRLVQAFQYTDKHGEVCPAGWKPGSETIIPDPAGKLKYFDKLN
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2347
R free: 0.2717
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.1mM MES (pH5.6), 16% PEG 400
Matthews coefficient: 2.7
Solvent content (%): 54.39
Release date: 2016-10-12
Crystal Structure Analysis of TAF1 Bromodomain (PDB entry 6P3A)
Macromolecule: Transcription initiation factor TFIID subunit 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 137 residues
Sequence: SMDDDQVAFSFILDNIVTQKMMAVPDSWPFHHPVNKKFVPDYYKVIVNPMDLETIRKNISKHKYQSRESFLDDVNLILANSVKYNGPESQYTKTAQEIVNVCYQTLTEYDEHLTQLEKDICTAKEAALEEAELESLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.99
R work: 0.2548
R free: 0.2862
Average B factor: 103.9829
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG8000, Tris pH 8.0
Matthews coefficient: 3.95
Solvent content (%): 68.84
Ligand: 4-{[(3R)-1-(but-3-en-1-yl)-3-methyl-4-(oxan-4-yl)-2-oxo-1,2,3,4-tetrahydropyrido[2,3-b]pyrazin-6-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide (NQP)
Ligand formula: C31 H42 N6 O4
Ligand molecular weight: 562.703
Ligand SMILES: CC1C(=O)N(c2ccc(nc2N1C3CCOCC3)Nc4ccc(cc4OC)C(=O)NC5CCN(CC5)C)CCC=C
Ligand InChI: InChI=1S/C31H42N6O4/c1-5-6-15-36-26-9-10-28(34-29(26)37(21(2)31(36)39)24-13-18-41-19-14-24)33-25-8-7-22(20-27(25)40-4)30(38)32-23-11-16-35(3)17-12-23/h5,7-10,20-21,23-24H,1,6,11-19H2,2-4H3,(H,32,38)(H,33,34)/t21-/m1/s1
Release date: 2020-05-27
DLK in complex with inhibitor 5-(1-isopropyl-5-(1-(oxetan-3-yl)piperidin-4-yl)-1H-pyrazol-3-yl)-3-(trifluoromethyl)pyridin-2-amine (compound 7) (PDB entry 5VO2)
Macromolecule: Mitogen-activated protein kinase kinase kinase 12
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 300 residues
Sequence: MGSEDLWEVPFEEILDLQWVGSGAQGAVFLGRFHGEEVAVKKVRDLKETDIKHLRKLKHPNIITFKGVCTQAPCYCILMEFCAQGQLYEVLRAGRPVTPSLLVDWSMGIAGGMNYLHLHKIIHRDLKSPNMLITYDDVVKISDFGTSKELSDKSTKMSFAGTVAWMAPEVIRNEPVSEKVDIWSFGVVLWELLTGEIPYKDVDSSAIIWGVGSNSLHLPVPSSCPDGFKILLRQCWNSKPRNRPSFRQILLHLDIASADVLSTPQETYFKSQAEWREEVKLHFEKIKSEGTGNSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.96
R work: 0.1695
R free: 0.2637
Average B factor: 34.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.7
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.2 M Mg Acetate, 0.1 M Hepes pH 7.7
Matthews coefficient: 1.93
Solvent content (%): 36.31
Ligand: 5-{5-[1-(oxetan-3-yl)piperidin-4-yl]-1-(propan-2-yl)-1H-pyrazol-3-yl}-3-(trifluoromethyl)pyridin-2-amine (9FV)
Ligand formula: C20 H26 F3 N5 O
Ligand molecular weight: 409.449
Ligand SMILES: CC(C)n1c(cc(n1)c2cc(c(nc2)N)C(F)(F)F)C3CCN(CC3)C4COC4
Ligand InChI: InChI=1S/C20H26F3N5O/c1-12(2)28-18(13-3-5-27(6-4-13)15-10-29-11-15)8-17(26-28)14-7-16(20(21,22)23)19(24)25-9-14/h7-9,12-13,15H,3-6,10-11H2,1-2H3,(H2,24,25)
Release date: 2017-10-04
Xray structure of human furin bound with the 2,5-dideoxystreptamine derived small molecule inhibitor 1n (PDB entry 5MIM)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 482 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1647
R free: 0.1838
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100 MM MES, 200 MM K/NAH2PO4, PH 5.5-6.0, 3-4 M NACL, 3% DMSO; RESERVOIR SOLUTION: 3-4 M NACL
Matthews coefficient: 3.75
Solvent content (%): 67.2
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: 2017-05-10
Crystal structure of human CDK8/CYCC in complex with BI-1347 (PDB entry 6QTG)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 405 residues
Sequence: GSMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPGNQDSSHTQGPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.201
R free: 0.231
Average B factor: 56.98
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 32-38% Morpheus Precipitant Mix 4
10 mmol/L Morpheus Buffer System 1
100 mM Morpheus Amino Acids Mix 2% DMSO
Matthews coefficient: 2.69
Solvent content (%): 54.33
Ligand: 2-[4-(4-isoquinolin-4-ylphenyl)pyrazol-1-yl]-~{N},~{N}-dimethyl-ethanamide (JH8)
Ligand formula: C22 H20 N4 O
Ligand molecular weight: 356.42
Ligand SMILES: CN(C)C(=O)Cn1cc(cn1)c2ccc(cc2)c3cncc4c3cccc4
Ligand InChI: InChI=1S/C22H20N4O/c1-25(2)22(27)15-26-14-19(12-24-26)16-7-9-17(10-8-16)21-13-23-11-18-5-3-4-6-20(18)21/h3-14H,15H2,1-2H3
Release date: 2020-03-18
Crystal structure of human CDK8/CYCC in complex with BI 919811 (PDB entry 6QTJ)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 405 residues
Sequence: GSMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEEEPDDKGDKKNQQQQQGNNHTNGTGHPGNQDSSHTQGPPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.185
R free: 0.22
Average B factor: 54.23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 32-38% Morpheus Precipitant Mix 4
10 mmol/L Morpheus Buffer System 1  100 mM Morpheus Amino Acids Mix 
2% DMSO
Matthews coefficient: 2.72
Solvent content (%): 54.7
Ligand: ~{N},~{N}-dimethyl-2-[4-[4-(2,6-naphthyridin-4-yl)phenyl]pyrazol-1-yl]ethanamide (JHK)
Ligand formula: C21 H19 N5 O
Ligand molecular weight: 357.408
Ligand SMILES: CN(C)C(=O)Cn1cc(cn1)c2ccc(cc2)c3cncc4c3cncc4
Ligand InChI: InChI=1S/C21H19N5O/c1-25(2)21(27)14-26-13-18(10-24-26)15-3-5-16(6-4-15)19-12-23-9-17-7-8-22-11-20(17)19/h3-13H,14H2,1-2H3
Release date: 2020-03-18
Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine (PDB entry 5AHG)
Macromolecule: THROMBIN HEAVY CHAIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 258 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.24
R work: 0.123
R free: 0.144
Average B factor: 19.9
Crystallization pH: 7.5
Crystal growth procedure: SEE MATERIAL AND METHODS SECTION OF PUBLICATION, pH 7.5
Matthews coefficient: 2.47
Solvent content (%): 50.2
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2015-08-26
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z86622311 (PDB entry 5RW7)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.23
R work: 0.1786
R free: 0.1954
Average B factor: 16.894
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.69
Ligand: 3-chloro-N-(1,2-oxazol-3-yl)benzamide (WMY)
Ligand formula: C10 H7 Cl N2 O2
Ligand molecular weight: 222.628
Ligand SMILES: c1cc(cc(c1)Cl)C(=O)Nc2ccon2
Ligand InChI: InChI=1S/C10H7ClN2O2/c11-8-3-1-2-7(6-8)10(14)12-9-4-5-15-13-9/h1-6H,(H,12,13,14)
Release date: 2020-11-11