satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the human phosphoserine aminotransferase (PSAT) in complex with O-phosphoserine (PDB entry 8A5W)
Macromolecule: Phosphoserine aminotransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.6.1.52
Sequence length: 365 residues
Sequence: QVVNFGPGPAKLPHSVLLEIQKELLDYKGVGISVLEMSHRSSDFAKIINNTENLVRELLAVPDNYKVIFLQGGGCGQFSAVPLNLIGLKAGRCADYVVTGAWSAKAAEEAKKFGTINIVHPKLGSYTKIPDPSTWNLNPDASYVYYCANETVHGVEFDFIPDVKGAVLVCDMSSNFLSKPVDVSKFGVIFAGAQKNVGSAGVTVVIVRDDLLGFALRECPSVLEYKVQAGNSSLYNTPPCFSIYVMGLVLEWIKNNGGAAAMEKLSSIKSQTIYEIIDNSQGFYVCPVEPQNRSKMNIPFRIGNAKGDDALEKRFLDKALELNMLSLKGHRSVGGIRASLYNAVTIEDVQKLAAFMKKFLEMHQL
Oligomeric state: Homo 8-mer
Stoichiometry: A8
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.78
R work: 0.1821
R free: 0.2276
Average B factor: 46.91
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Na2SO4, 0.1 M Bis Tris Propane, pH 7,5, 20 % PEG 3350
Matthews coefficient: 3.01
Solvent content (%): 59.1
Ligand: (2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid (E1U)
Ligand formula: C11 H16 N2 O11 P2
Ligand molecular weight: 414.199
Ligand SMILES: Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(COP(=O)(O)O)C(=O)O)O
Ligand InChI: InChI=1S/C11H16N2O11P2/c1-6-10(14)8(7(2-12-6)4-23-25(17,18)19)3-13-9(11(15)16)5-24-26(20,21)22/h2-3,9,14H,4-5H2,1H3,(H,15,16)(H2,17,18,19)(H2,20,21,22)/t9-/m0/s1
Release date: 2023-03-29
Human cyclic GMP-AMP synthase (cGAS) in complex with Compound F2 (PDB entry 5VDU)
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): 2.729
R work: 0.2223
R free: 0.2521
Average B factor: 65.174
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: 2.57
Solvent content (%): 52.1
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: 2017-09-27
Crystal structure of USP7 in complex with its inhibitor (PDB entry 7XPY)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 548 residues
Sequence: GPLGSEAHLYMQVQIVAEDQFCGHQGNDMYDEEKVKYTVFKVLKNSSLAEFVQSLSQTMGFPQDQIRLWPMQARSNGTKRPAMLDNEADGNKTMIELSDNENPWTIFLETVDPELAASGATLPKFDKDHDVMLFLKMYDPKTRSLNYCGHIYTPISCKIRDLLPVMCDRAGFIQDTSLILYEEVKPNLTERIQDYDVSLDKALDELMDGDIIVFQKDDPENDNSELPTAKEYFRDLYHRVDVIFCDKTIPNDPGFVVTLSNRMNYFQVAKTVAQRLNTDPMLLQFFKSQGYRDGPGNPLRHNYEGTLRDLLQFFKPRQPKKLYYQQLKMKITDFENRRSFKCIWLNSQFREEEITLYPDKHGCVRDLLEECKKAVELGEKASGKLRLLEIVSYKIIGVHQEDELLECLSPATSRTFRIEEIPLDQVDIDKENEMLVTVAHFHKEVFGTFGIPFLLRIHQGEHFREVMKRIQSLLDIQEKEFEKFKFAIVMMGRHQYINEDEYEVNLKDFEPQPGNMSHPRPWLGLDHFNKAPKRSRYTYLEKAIKIHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.224
R free: 0.2658
Average B factor: 80.329
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 2% v/v Tacsimate pH 7.0, 0.1 M Imidazole pH 7.0, 8% w/v Polyethylene glycol 3350, 5% v/v 2-Propanol
Matthews coefficient: 3.68
Solvent content (%): 66.57
Ligand: [(3S,3aR,4R,6Z,9S,10E,11aR)-9-acetyloxy-6-(acetyloxymethyl)-3,10-dimethyl-2-oxidanylidene-3a,4,5,8,9,11a-hexahydro-3H-cyclodeca[b]furan-4-yl] (E)-2-methyl-4-oxidanyl-but-2-enoate (EIB)
Ligand formula: C24 H32 O9
Ligand molecular weight: 464.505
Ligand SMILES: CC1C2C(CC(=CCC(C(=CC2OC1=O)C)OC(=O)C)COC(=O)C)OC(=O)C(=CCO)C
Ligand InChI: InChI=1S/C24H32O9/c1-13(8-9-25)23(28)32-21-11-18(12-30-16(4)26)6-7-19(31-17(5)27)14(2)10-20-22(21)15(3)24(29)33-20/h6,8,10,15,19-22,25H,7,9,11-12H2,1-5H3/b13-8+,14-10+,18-6-/t15-,19-,20+,21+,22-/m0/s1
Release date: 2022-08-24
TEV Cleaved Human ATP Citrate Lyase Bound to 4S Hydroxycitrate (PDB entry 5TET)
Macromolecule: ATP-citrate synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.3.8
Sequence length: 431 residues
Sequence: MSAKAISEQTGKELLYKFICTTSAIQNRFKYARVTPDTDWARLLQDHPWLLSQNLVVKPDQLIKRRGKLGLVGVNLTLDGVKSWLKPRLGQEATVGKATGFLKNFLIEPFVPHSQAEEFYVCIYATREGDYVLFHHEGGVDVGDVDAKAQKLLVGVDEKLNPEDIKKHLLVHAPEDKKEILASFISGLFNFYEDLYFTYLEINPLVVTKDGVYVLDLAAKVDATADYICKVKWGDIEFPPPFGREAYPEEAYIADLDAKSGASLKLTLLNPKGRIWTMVAGGGASVVYSDTICDLGGVNELANYGEYSGAPSEQQTYDYAKTILSLMTREKHPDGKILIIGGSIANFTNVAATFKGIVRAIRDYQGPLKEHEVTIFVRRGGPNYQEGLRVMGEVGKTTGIPIHVFGTETHMTAIVGMALGHRPIPENLYFQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.156
R free: 0.213
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 294
Crystal growth procedure: 12.5% of P3350, 100 mM TrisHCL pH 7.5, 125 mM ammonium phosphate pH 7.5
Matthews coefficient: 2.68
Solvent content (%): 54.02
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: 2017-08-09
Crystal Structure of human formylglycine generating enzyme (PDB entry 5SSY)
Macromolecule: Formylglycine-generating enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.8.3.7
Sequence length: 323 residues
Sequence: ADLGSSMEFEANAPGPVPGERQLAHSKMVPIPAGVFTMGTDDPQIKQDGEAPARRVTIDAFYMDAYEVSNTEFEKFVNSTGYLTEAEKFGDSFVFEGMLSEQVKTNIQQAVAAAPWWLPVKGANWRHPEGPDSTILHRPDHPVLHVSWNDAVAYCTWAGKRLPTEAEWEYSCRGGLHNRLFPWGNKLQPKGQHYANIWQGEFPVTNTGEDGFQGTAPVDAFPPNGYGLYNIVGNAWEWTSDWWTVHHSVEETLNPKGPPSGKDRVKKGGSYMCHRSYCYRYRCAARSQNTPDSSASNLGFRCAADRLPTMDSGRGSHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.2116
R free: 0.2371
Average B factor: 15.3565
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 9.6 mg/mL protein in 20mM Tris/HCl pH8.0 mixed 1:1 with reservoir 0.1M Tris/HCl pH 8.5, 20-25% PEG4000, 0.2-0.3M CaCl2
Matthews coefficient: 2.04
Solvent content (%): 39.63
Ligand: methyl N-acetyl-L-cysteinate (UG6)
Ligand formula: C6 H11 N O3 S
Ligand molecular weight: 177.221
Ligand SMILES: CC(=O)NC(CS)C(=O)OC
Ligand InChI: InChI=1S/C6H11NO3S/c1-4(8)7-5(3-11)6(9)10-2/h5,11H,3H2,1-2H3,(H,7,8)/t5-/m0/s1
Release date: 2023-08-23
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with XST00000754b (PDB entry 7GTF)
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): 1.97
R work: 0.2155
R free: 0.2592
Average B factor: 40.535
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.38
Solvent content (%): 63.63
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2024-01-24
Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors (PDB entry 6P6G)
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): 1.59
R work: 0.1723
R free: 0.2002
Average B factor: 23.7103
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: Sitting Drop, Linbro tray, room temp, reservoir is 10% PEG 3350, 0.2M MgOAc ,
protein:reservoir is 1:1,
streak seed
soaking: 2ul 20%PEG 3350, 0.4M MgOAc added to 2ul protein, mix and add 0.3ul to drop, store at 295
Matthews coefficient: 2.22
Solvent content (%): 44.53
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: 2020-01-15
Crystal structure of JAK3 in complex with Delgocitinib (PDB entry 7C3N)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 315 residues
Sequence: GSQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGCERDVPALCRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSRGCETHAFTAHPEGKHHSLSFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.1685
R free: 0.1943
Average B factor: 27.97
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 50mM Pipes pH6.0, 1.1M sodium malonate, 1.6% glycerol, 10mM DTT
Matthews coefficient: 2.05
Solvent content (%): 40.06
Ligand: 3-[(3S,4R)-3-methyl-7-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1,7-diazaspiro[3.4]octan-1-yl]-3-oxidanylidene-propanenitrile (FHX)
Ligand formula: C16 H18 N6 O
Ligand molecular weight: 310.354
Ligand SMILES: CC1CN(C12CCN(C2)c3c4cc[nH]c4ncn3)C(=O)CC#N
Ligand InChI: InChI=1S/C16H18N6O/c1-11-8-22(13(23)2-5-17)16(11)4-7-21(9-16)15-12-3-6-18-14(12)19-10-20-15/h3,6,10-11H,2,4,7-9H2,1H3,(H,18,19,20)/t11-,16-/m0/s1
Release date: 2020-06-24
Crystal Structure of c-Cbl TKBD in complex with SPRY2 peptide (36-60, pY55) Refined to 1.8 A Resolution (P21 form) (PDB entry 5HKZ)
Macromolecule: E3 ubiquitin-protein ligase CBL
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 308 residues
Sequence: SNAPPGTVDKKMVEKCWKLMDKVVRLCQNPKLALKNSPPYILDLLPDTYQHLRTILSRYEGKMETLGENEYFRVFMENLMKKTKQTISLFKEGKERMYEENSQPRRNLTKLSLIFSHMLAELKGIFPSGLFQGDTFRITKADAAEFWRKAFGEKTIVPWKSFRQALHEVHPISSGLEAMALKSTIDLTCNDYISVFEFDIFTRLFQPWSSLLRNWNSLAVTHPGYMAFLTYDEVKARLQKFIHKPGSYIFRLSCTRLGQWAIGYVTADGNILQTIPHNKPLFQALIDGFREGFYLFPDGRNQNPDLTG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1618
R free: 0.2126
Average B factor: 25.0576
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 25% (w/v) PEG 2000 MME, 0.1M HEPES
Matthews coefficient: 2.04
Solvent content (%): 39.71
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-01-18
STRUCTURE OF RET PROTEIN TYROSINE KINASE DOMAIN IN COMPLEX WITH NINTEDANIB (PDB entry 6NEC)
Macromolecule: Proto-oncogene tyrosine-protein kinase receptor Ret
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 314 residues
Sequence: GPLSLSVDAFKILEDPKWEFPRKNLVLGKTLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYGSLRGFLRESRKVGPGYLGSGGSRNSSSLDHPDERALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDSYVKRSQGRIPVKWMAIESLFDHIYTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVKRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.19428
R free: 0.23188
Average B factor: 41.026
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 297
Crystal growth procedure: 2.6 M Na FORMATE
0.1M Na CITRATE PH5.5
Matthews coefficient: 2.23
Solvent content (%): 44.95
Ligand: methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate (XIN)
Ligand formula: C31 H33 N5 O4
Ligand molecular weight: 539.625
Ligand SMILES: CN1CCN(CC1)CC(=O)N(C)c2ccc(cc2)NC(=C3c4ccc(cc4NC3=O)C(=O)OC)c5ccccc5
Ligand InChI: InChI=1S/C31H33N5O4/c1-34-15-17-36(18-16-34)20-27(37)35(2)24-12-10-23(11-13-24)32-29(21-7-5-4-6-8-21)28-25-14-9-22(31(39)40-3)19-26(25)33-30(28)38/h4-14,19,32H,15-18,20H2,1-3H3,(H,33,38)/b29-28-
Release date: 2019-06-05
Thrombin in complex with 2-amino-1-(4-bromophenyl)ethan-1-one (j10) (PDB entry 6YSJ)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1338
R free: 0.1676
Average B factor: 24.8816
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20mM sodium dihydrogen phosphate pH 7.5
350mM NaCl
27% PEG 8000
Matthews coefficient: 2.76
Solvent content (%): 55.48
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: 2021-05-12
Human PARP16 (ARTD15) IN COMPLEX WITH EB-47 (PDB entry 6HXR)
Macromolecule: Mono [ADP-ribose] polymerase PARP16
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 298 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGWAAAREAAGRDMLAADLRCSLFASALQSYKRDSVLRPFPASYARGDCKDFEALLADASKLPNLKELLQSSGDNHKRAWDLVSWILSSKVLTIHSAGKAEFEKIQKLTGAPHTPVPAPDFLFEIEYFDPANAKFYETKGERDLIYAFHGSRLENFHSIIHNGLHCHLNKTSLFGEGTYLTSDLSLALIYSPHGHGWQHSLLGPILSCVAVCEVIDHPDVKCQTKKKDSKEIDRRRARIKHSEGGDIPPKYFVVTNNQLLRVKYLLVYSQKPPKRA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.1993
R free: 0.2297
Average B factor: 91.94
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 25% Poly(ethylene glycol) 3350, 0.2M ammonium acetate, 0.1M Bis-Tris, 1mM EB-47
Matthews coefficient: 2.71
Solvent content (%): 54.66
Ligand: 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide (UHB)
Ligand formula: C24 H27 N9 O6
Ligand molecular weight: 537.528
Ligand SMILES: c1cc2c(c(c1)NC(=O)CN3CCN(CC3)C(=O)C4C(C(C(O4)n5cnc6c5ncnc6N)O)O)CNC2=O
Ligand InChI: InChI=1S/C24H25N9O6/c25-20-16-21(28-10-27-20)33(11-29-16)24-18(36)17(35)19(39-24)23(38)32-6-4-31(5-7-32)9-15(34)30-14-3-1-2-12-13(14)8-26-22(12)37/h1-3,8,10-11,17-19,24,35-36H,4-7,9H2,(H,26,37)(H2,25,27,28)/b30-14-/t17-,18+,19-,24+/m0/s1
Release date: 2019-10-30
Fragment-Based Discovery of a Novel Bruton's Tyrosine Kinase Inhibitor (PDB entry 7N5X)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 283 residues
Sequence: GPLPGKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1662
R free: 0.1877
Average B factor: 18.02
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% polyethylene glycol 4000, 20% glycerol, 0.1M imidazole/MES, pH 6.5 and 0.12M alcohol mixture
Matthews coefficient: 2.22
Solvent content (%): 44.61
Ligand: S-1,2-PROPANEDIOL (PGO)
Ligand formula: C3 H8 O2
Ligand molecular weight: 76.094
Ligand SMILES: CC(CO)O
Ligand InChI: InChI=1S/C3H8O2/c1-3(5)2-4/h3-5H,2H2,1H3/t3-/m0/s1
Release date: 2021-09-08
The structure of ERK2 in complex with dual inhibitor ASTX029 (PDB entry 7AUV)
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: 0.167
R free: 0.229
Average B factor: 29.57
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 291
Crystal growth procedure: 0.2M (NH4)2SO4
32% MPEG 2000
.02M Mercaptoethanol
.1M pH=7.2 HEPES/NaOH
Matthews coefficient: 2.33
Solvent content (%): 47.31
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: 2021-10-06
Hydrocarbon-Stapled Paxillin Peptide Bound to the Focal Adhesion Targeting (FAT) Domain of the Focal Adhesion Kinase (FAK) (PDB entry 6PW8)
Macromolecule: Focal adhesion kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 126 residues
Sequence: DKVYENVTGLVKAVIEMSSKIQPAPPEEYVPMVKEVGLALRTLLATVDETIPLLPASTHREIEMAQKLLNSDLGELINKMKLAQQYVMTSLQQEYKKQMLTAAHALAVDAKNLLDVIDQARLKMLG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2172
R free: 0.2495
Average B factor: 38.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.02 M zinc chloride, 20% PEG3350
Matthews coefficient: 2.15
Solvent content (%): 42.85
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: 2020-07-22
CO2 release in human carbonic anhydrase II crystals: reveal histidine 64 and solvent dynamics (PDB entry 5YUJ)
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): 1.25
R work: 0.09981
R free: 0.12957
Average B factor: 16.137
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.3M sodium citrate, 100mM TrisHCl pH 7.8
Matthews coefficient: 2.08
Solvent content (%): 40.9
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: 2018-08-01
Human REXO2 bound to pAG (PDB entry 6N6K)
Macromolecule: RNA exonuclease 2 homolog,Small fragment nuclease
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 205 residues
Sequence: MAAGESMAQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILAEGPNLIIKQPDELLDSMSDWCKEHHGKSGLTKAVKESTITLQQAEYEFLSFVRQQTPPGLCPLAGNSVHEDKKFLDKYMPQFMKHLHYRIIDVSTVKELCRRWYPEEYEFAPKKAASHRALDDISESIKELQFYRNNIFKKKIDEKKRKIIENGENEKTVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.418
R work: 0.1531
R free: 0.1724
Average B factor: 22.7865
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M sodium malonate (pH 5.5) and 15-20% polyethylene glycol 3350, 25% glycerol
Matthews coefficient: 2.55
Solvent content (%): 51.72
Ligand: MALONATE ION (MLI)
Ligand formula: C3 H2 O4
Ligand molecular weight: 102.046
Ligand SMILES: C(C(=O)[O-])C(=O)[O-]
Ligand InChI: InChI=1S/C3H4O4/c4-2(5)1-3(6)7/h1H2,(H,4,5)(H,6,7)/p-2
Release date: 2019-06-12
RPA70N-RAD9 fusion (PDB entry 8JZY)
Macromolecule: Cell cycle checkpoint control protein RAD9A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.11.2
Sequence length: 19 residues
Sequence: DDFANDDIDSYMIAMETTI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1848
R free: 0.2004
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG 3350,  sodium phosphate
Matthews coefficient: 2.34
Solvent content (%): 47.48
Release date: 2023-09-13
The crystal structure of CK2alpha in complex with compound 26 (PDB entry 5OTH)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 352 residues
Sequence: GSMDIEFDDDADDDGSGSGSGSGSSGPVPSRARVYTDVNTHRPSEYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVK
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.24
R free: 0.265
Average B factor: 49.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 112.5mM Mes pH 6.5, 35% glycerol ethoxylate, 180 mM ammonium acetate
Matthews coefficient: 2.2
Solvent content (%): 44.03
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: 2018-02-28