satarupa22/MacromolecularLigandDB huggingface dataset:
Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active (PDB entry 5DKW)
Macromolecule: DNA polymerase lambda
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 327 residues
Sequence: ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.689
R work: 0.1837
R free: 0.2327
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES, 30%(v/v) Jeffamine ED-2100 Reagent
Matthews coefficient: 3.66
Solvent content (%): 69.64
Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP)
Ligand formula: C10 H16 N5 O12 P3
Ligand molecular weight: 491.182
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2016-02-24
PP2Ca (PDB entry 4RA2)
Macromolecule: Protein phosphatase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 367 residues
Sequence: GAFLDKPKMEKHNAQGQGNGLRYGLSSMQGWRVEMEDAHTAVIGLPSGLESWSFFAVYDGHAGSQVAKYCCEHLLDHITNNQDFKGSAGAPSVENVKNGIRTGFLEIDEHMRVMSEKKHGADRSGSTAVGVLISPQHTYFINCGDSRGLLCRNRKVHFFTQDHKPSNPLEKERIQNAGGSVMIQRVNGSLAVSRALGDFDYKCVHGKGPTEQLVSPEPEVHDIERSEEDDQFIILACDGIWDVMGNEELCDFVRSRLEVTDDLEKVCNEVVDTCLYKGSRDNMSVILICFPNAPKVSPEAVKKEAELDKYLECRVEEIIKKQGEGVPDLVHVMRTLASENIPSLPPGGELASKRNVIEAVYNRLNPY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.196
R free: 0.224
Crystallization pH: 5.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 15(v/v)% PEG8000, pH 5.5, 50mM K2HPO4, 15% 2mMDTT, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K
Matthews coefficient: 3.07
Solvent content (%): 59.97
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2015-05-13
Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102305 (PDB entry 5QIR)
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): 1.43
R work: 0.1341
R free: 0.182
Average B factor: 18.915
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: 2.35
Solvent content (%): 47.63
Ligand: N-[(4-fluoro-3-methylphenyl)methyl]acetamide (J5D)
Ligand formula: C10 H12 F N O
Ligand molecular weight: 181.207
Ligand SMILES: Cc1cc(ccc1F)CNC(=O)C
Ligand InChI: InChI=1S/C10H12FNO/c1-7-5-9(3-4-10(7)11)6-12-8(2)13/h3-5H,6H2,1-2H3,(H,12,13)
Release date: 2019-12-18
PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13964a (PDB entry 5R5J)
Macromolecule: Uridine diphosphate glucose pyrophosphatase NUDT22
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.45
Sequence length: 304 residues
Sequence: SMDPEVTLLLQCPGGGLPQEQIQAELSPAHDRRPLPGGDEAITAIWETRLKAQPWLFDAPKFRLHSATLAPIGSRGPQLLLRLGLTSYRDFLGTNWSSSAAWLRQQGATDWGDTQAYLADPLGVGAALATADDFLVFLRRSRQVAEAPGLVDVPGGHPEPQALCPGGSPQHQDLAGQLVVHELFSSVLQEICDEVNLPLLTLSQPLLLGIARNETSAGRASAEFYVQCSLTSEQVRKHYLSGGPEAHESTGIFFVETQNVRRLPETEMWAELCPSAKGAIILYNRVQGSPTGAALGSPALLPPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1783
R free: 0.2361
Average B factor: 35.273
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol
Matthews coefficient: 2.02
Solvent content (%): 39.15
Ligand: 3-[(5-methylthiophen-2-yl)methylamino]benzoic acid (MH5)
Ligand formula: C13 H13 N O2 S
Ligand molecular weight: 247.313
Ligand SMILES: Cc1ccc(s1)CNc2cccc(c2)C(=O)O
Ligand InChI: InChI=1S/C13H13NO2S/c1-9-5-6-12(17-9)8-14-11-4-2-3-10(7-11)13(15)16/h2-7,14H,8H2,1H3,(H,15,16)
Release date: 2020-07-01
Factor XIa in complex with the inhibitor methyl (4-{4-chloro-2-[(1S)-1-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-2-phenylethyl]-1H-imidazol-5-yl}phenyl)carbamate (PDB entry 4Y8X)
Macromolecule: Coagulation factor XIa
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.1575
R free: 0.1644
Average B factor: 27.12
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 26% w/v MEPEG2000, 200 mM ammonium sulfate (crystals were grown at pH4.6 and transferred to pH 7 prior to soaking with compound)
Matthews coefficient: 3.59
Solvent content (%): 65.73
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: 2015-05-27
Human cyclic GMP-AMP synthase (cGAS) in complex with 2',3'-cGAMP (PDB entry 5VDP)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 363 residues
Sequence: MGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1972
R free: 0.2429
Average B factor: 47.1048
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 18-20% PEG 3350, 0.2 M ammonium citrate pH 7
Matthews coefficient: 2.47
Solvent content (%): 50.19
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: 2017-09-27
Crystal Structure of ERK2 in complex with N-cyclohexyl-9H-purin-6-amine (PDB entry 4QP4)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 369 residues
Sequence: MGSHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1866
R free: 0.2352
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% PEG3350, 0.2 M proline, and 0.1 M HEPES pH7.5, in a 24-well Linbro plates incubated at 4C, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Matthews coefficient: 2
Solvent content (%): 38.38
Ligand: N-cyclohexyl-9H-purin-6-amine (36O)
Ligand formula: C11 H15 N5
Ligand molecular weight: 217.27
Ligand SMILES: c1[nH]c2c(n1)c(ncn2)NC3CCCCC3
Ligand InChI: InChI=1S/C11H15N5/c1-2-4-8(5-3-1)16-11-9-10(13-6-12-9)14-7-15-11/h6-8H,1-5H2,(H2,12,13,14,15,16)
Release date: 2015-09-23
Co-crystal structure of human SMYD3 with an aza-SAH compound (PDB entry 5HI7)
Macromolecule: Histone-lysine N-methyltransferase SMYD3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 432 residues
Sequence: GSFTMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1984
R free: 0.2257
Average B factor: 36
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: SMYD3 crystallization and soaking of GSK2807: SMYD3 (1-428) expressed in baculovirus and with SAH in the SAM-binding site was crystallized in sitting drops at 22C using 1uL fresh protein at 8.9mg/mL with the addition of 1uL mother liquor (200mM MgOAc Tetrahydrate, 20% PEG 3350). Crystals grew to a large size but varied in quantity when set up in replicates.  A seed stock was formed from these crystals and added at 20% to the mother liquor solution prior to plate setup. Crystals of large size were then created with 1.3uL protein and 1.3uL of mother liquor containing seeds in a sitting drop MRC-2 plate (Hampton Research).  Crystal nucleation occurred overnight and reached maximum size in 4 days
Matthews coefficient: 2.12
Solvent content (%): 42.1
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: 2016-03-30
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with scyllo-inositol 1,2,3,5-tetrakisphosphate/ADP/Mn (PDB entry 8PP9)
Macromolecule: Inositol-trisphosphate 3-kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.127
Sequence length: 279 residues
Sequence: GSHMSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.19381
R free: 0.20989
Average B factor: 39.609
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.81 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. 
Protein:precipitant ratio 1:1. 
Protein concentration: 17 mg/ml. 
Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. 
Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 5 mM ligand, 3 mM ADP and 3 mM MnCl2.
Matthews coefficient: 2.69
Solvent content (%): 54.38
Ligand: scyllo-inositol 1,2,3,5-tetrakisphosphate (4IM)
Ligand formula: C6 H16 O18 P4
Ligand molecular weight: 500.075
Ligand SMILES: C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C6H16O18P4/c7-1-3(21-25(9,10)11)2(8)5(23-27(15,16)17)6(24-28(18,19)20)4(1)22-26(12,13)14/h1-8H,(H2,9,10,11)(H2,12,13,14)(H2,15,16,17)(H2,18,19,20)/t1-,2+,3-,4+,5-,6-
Release date: 2024-02-28
Crystal structure of the human bromodomain of EP300 bound to the inhibitor XDM-CBP (PDB entry 5NU5)
Macromolecule: Histone acetyltransferase p300
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 116 residues
Sequence: SMIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKSPMDLSTIKRKLDTGQYQEPWQYVDDIWLMFNNAWLYNRKTSRVYKYCSKLSEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1624
R free: 0.1854
Average B factor: 20.09
Crystallization method: EVAPORATION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: KSCN, NaBr, PEG 6000, PEG 8000, PEG 10000
Matthews coefficient: 2.25
Solvent content (%): 45.37
Ligand: ~{N}-[[2,8-bis(oxidanyl)naphthalen-1-yl]methyl]-4-ethanoyl-3-ethyl-5-methyl-1~{H}-pyrrole-2-carboxamide (99E)
Ligand formula: C21 H22 N2 O4
Ligand molecular weight: 366.41
Ligand SMILES: CCc1c(c([nH]c1C(=O)NCc2c(ccc3c2c(ccc3)O)O)C)C(=O)C
Ligand InChI: InChI=1S/C21H22N2O4/c1-4-14-18(12(3)24)11(2)23-20(14)21(27)22-10-15-16(25)9-8-13-6-5-7-17(26)19(13)15/h5-9,23,25-26H,4,10H2,1-3H3,(H,22,27)
Release date: 2017-08-16
Bruton's tyrosine kinase in complex with compound 34 (PDB entry 8FLV)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 283 residues
Sequence: GPLGSKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1941
R free: 0.2181
Average B factor: 17.64
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: bis-tris, ammonium salt, PEG
Matthews coefficient: 2.28
Solvent content (%): 46.01
Ligand: 2-(3,5-dichloroanilino)-1-{(3R)-3-[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}ethan-1-one (ZB9)
Ligand formula: C20 H22 Cl2 N6 O
Ligand molecular weight: 433.334
Ligand SMILES: CN(c1c2cc[nH]c2ncn1)C3CCCN(C3)C(=O)CNc4cc(cc(c4)Cl)Cl
Ligand InChI: InChI=1S/C20H22Cl2N6O/c1-27(20-17-4-5-23-19(17)25-12-26-20)16-3-2-6-28(11-16)18(29)10-24-15-8-13(21)7-14(22)9-15/h4-5,7-9,12,16,24H,2-3,6,10-11H2,1H3,(H,23,25,26)/t16-/m1/s1
Release date: 2023-04-05
Crystal structure of human protein O-mannose beta-1,2-N-acetylglucosaminyltransferase in complex with Mn, UDP and Mannosyl-peptide (PDB entry 5GGI)
Macromolecule: mannosyl-peptide
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 11 residues
Sequence: XAAPTPVAAPX
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1989
R free: 0.2385
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: NaKPO4
Matthews coefficient: 2.81
Solvent content (%): 56.2
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2016-08-10
AMP-activated protein kinase bound to pharmacological activator R734 (PDB entry 6C9F)
Macromolecule: 5'-AMP-activated protein kinase catalytic subunit alpha-1,5'-AMP-activated protein kinase catalytic subunit alpha-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 494 residues
Sequence: MGHHHHHHGSVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFPEDPSYSSTMIDDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAKDFYLATSPPDSFLDDHHLTRPHPERVPFLVAETPRARHTLDELNPQKSKHQGVRKAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTYSKMSLQLYQVDSRTYLLDFRSIDDELTPRPGSHTIEFFEMCANLIKILAQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.924
R work: 0.2279
R free: 0.2449
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M tri-sodium acetate pH 5.6, 0.2 M ammonium acetate, 15% w/v PEG 4000
Matthews coefficient: 3.78
Solvent content (%): 67.47
Ligand: 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide (R34)
Ligand formula: C24 H19 Cl N4 O3
Ligand molecular weight: 446.886
Ligand SMILES: Cc1ccc(cc1C(=O)NO)Oc2[nH]c3cc(c(cc3n2)c4ccc5c(c4)ccn5C)Cl
Ligand InChI: InChI=1S/C24H19ClN4O3/c1-13-3-5-16(10-17(13)23(30)28-31)32-24-26-20-11-18(19(25)12-21(20)27-24)14-4-6-22-15(9-14)7-8-29(22)2/h3-12,31H,1-2H3,(H,26,27)(H,28,30)
Release date: 2018-11-28
CRYSTAL STRUCTURE OF AP2 ASSOCIATED KINASE 1 COMPLEXED WITH (5P)-3-({(8R)-5-[(4-aminopiperidin-1-yl)methyl]pyrrolo[2,1-f][1,2,4]triazin-4-yl}amino)-5-[2-(propan-2-yl)-2H-tetrazol-5-yl]phenol (PDB entry 8GMD)
Macromolecule: AP2-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 318 residues
Sequence: MHHHHHHLVPRGSSTSGLGSGYIGRVFGIGRQQVTVDEVLAEGGFAIVFLVRTSNGMKCALKRMFVNNEHDLQVCKREIQIMRDLSGHKNIVGYIDSSINNVSSGDVWEVLILMDFCRGGQVVNLMNQRLQTGFTENEVLQIFCDTCEAVARLHQCKTPIIHRDLKVENILLHDRGHYVLCDFGSATNKFQNPQTEGVNAVEDEIKKYTTLSYRAPEMVNLYSGKIITTKADIWALGCLLYKLCYFTLPFGESQVAICDGNFTIPDNSRYSQDMHCLIRYMLEPDPDKRPDIYQVSYFSFKLLKKECPIPNVQNSPIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.232
R free: 0.25
Average B factor: 50.12
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 296
Crystal growth procedure: 1.2M AmSO4, 0.1M tri-Na Citrate pH 6.0, 3% isopropanol, 296K
Matthews coefficient: 3.08
Solvent content (%): 60.04
Ligand: (5P)-3-({(8R)-5-[(4-aminopiperidin-1-yl)methyl]pyrrolo[2,1-f][1,2,4]triazin-4-yl}amino)-5-[2-(propan-2-yl)-2H-tetrazol-5-yl]phenol (ZRR)
Ligand formula: C22 H28 N10 O
Ligand molecular weight: 448.524
Ligand SMILES: CC(C)n1nc(nn1)c2cc(cc(c2)O)Nc3c4c(ccn4ncn3)CN5CCC(CC5)N
Ligand InChI: InChI=1S/C22H28N10O/c1-14(2)32-28-21(27-29-32)16-9-18(11-19(33)10-16)26-22-20-15(3-8-31(20)25-13-24-22)12-30-6-4-17(23)5-7-30/h3,8-11,13-14,17,33H,4-7,12,23H2,1-2H3,(H,24,25,26)
Release date: 2023-07-12
Apo Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) (PDB entry 4U3Y)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 332 residues
Sequence: GSANDSPAKSLVDIDLSSLRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKLEINMLKKYSHHRNIATYYGAFIKKSPPGHDDQLWLVMEFCGAGSITDLVKNTKGNTLKEDWIAYISREILRGLAHLHIHHVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDYRSDLWSCGITAIEMAEGAPPLCDMHPMRALFLIPRNPPPRLKSKKWSKKFFSFIEGCLVKNYMQRPSTEQLLKHPFIRDQPNERQVRIQLKDHIDRTRKKRGEKDETEYEYSGSEEGNS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1826
R free: 0.2069
Average B factor: 23.83
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M potassium citrate, pH 8.3, 20% PEG 3350
Matthews coefficient: 1.99
Solvent content (%): 38.32
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: 2016-01-06
Crystal structure of mUCH37-hRPN13 CTD complex (PDB entry 4WLQ)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase isozyme L5
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 3.4.19.12
Sequence length: 328 residues
Sequence: MSSNAGEWCLMESDPGVFTELIKGFGCRGAQVEEIWSLEPESFEKLKPVHGLIFLFKWQPGEEPAGSVVQDSRLETIFFAKQVINNACATQAIVSVLLNCTHQDVHLGETLSEFKEFSQSFDAAMKGLALSNSDVIRQVHNSFARQQMFEFDTKTPAKEEDAFHFVSYVPVNGRLYELDGLREGPIDLGACNQDDWITAVRPVIEKRIQKYSEGEIRFNLMAIVSDRKMIYEQKIAELQRQLAEEPMDTDQGSTVLSAIQSEVARNQMLIEEEVQKLKRYKIENIRRKHNYLPFIMELLKTLAEHQQLIPLVEKAKEKQNAKKAQETK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.1918
R free: 0.278
Average B factor: 112.4345
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 277
Crystal growth procedure: 20% PEG 3350, 200 mM Mg(OAC)2,100 mM HEPES
Matthews coefficient: 2.99
Solvent content (%): 58.93
Release date: 2015-03-04
PDGFRA T674I mutant kinase domain in complex with avapritinib (PDB entry 8PQH)
Macromolecule: Platelet-derived growth factor receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 352 residues
Sequence: KQKPRYEIRWRVIESISPDGHEYIYVDPMQLPYDSRWEFPRDGLVLGRVLGSGAFGKVVEGTAYGLSRSQPVMKVAVKMLKPTARSSEKQALMSELKIMTHLGPHLNIVNLLGACTKSGPIYIIIEYCFYGDLVNYLHKNRDSFLSHKKKSMLDSEVKNLLSDDNSEGLTLLDLLSFTYQVARGMEFLASKNCVHRDLAARNVLLAQGKIVKICDFGLARDIMHDSNYVSKGSTFLPVKWMAPESIFDNLYTTLSDVWSYGILLWEIFSLGGTPYPGMMVDSTFYNKIKSGYRMAKPDHATSEVYEIMVKCWNSEPEKRPSFYHLSEIVENLLPGQYKKSYEKIHLDFLKSD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2184
R free: 0.2486
Average B factor: 78.98
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 10 mg/mL, 13% PEG3350, 200 mM KCl
Matthews coefficient: 2.02
Solvent content (%): 39.24
Ligand: Avapritinib (9JI)
Ligand formula: C26 H27 F N10
Ligand molecular weight: 498.558
Ligand SMILES: CC(c1ccc(cc1)F)(c2cnc(nc2)N3CCN(CC3)c4c5cc(cn5ncn4)c6cnn(c6)C)N
Ligand InChI: InChI=1S/C26H27FN10/c1-26(28,20-3-5-22(27)6-4-20)21-13-29-25(30-14-21)36-9-7-35(8-10-36)24-23-11-18(16-37(23)33-17-31-24)19-12-32-34(2)15-19/h3-6,11-17H,7-10,28H2,1-2H3/t26-/m0/s1
Release date: 2023-12-27
ERK5 in complex with a pyrrole inhibitor (PDB entry 5O7I)
Macromolecule: Mitogen-activated protein kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 358 residues
Sequence: GDVTFDVGDEYEIIETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKHFKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQAVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLAKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARREGIRQQIRFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.38
R work: 0.1805
R free: 0.2203
Average B factor: 59.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 5 % (v/v) PEG 6000, 0.1 M MES (pH 6.0), 5 mM DTT
Matthews coefficient: 3.05
Solvent content (%): 59.73
Ligand: 4-(2-bromanyl-6-fluoranyl-phenyl)carbonyl-~{N}-pyridin-3-yl-1~{H}-pyrrole-2-carboxamide (9N8)
Ligand formula: C17 H11 Br F N3 O2
Ligand molecular weight: 388.191
Ligand SMILES: c1cc(c(c(c1)Br)C(=O)c2cc([nH]c2)C(=O)Nc3cccnc3)F
Ligand InChI: InChI=1S/C17H11BrFN3O2/c18-12-4-1-5-13(19)15(12)16(23)10-7-14(21-8-10)17(24)22-11-3-2-6-20-9-11/h1-9,21H,(H,22,24)
Release date: 2018-06-20