satarupa22/MacromolecularLigandDB huggingface dataset:
The Fk1 domain of FKBP51 in complex with 2-(3-((1R)-1-(((2S)-1-(2-(5-chlorothiophen-2-yl)-2-cyclohexylacetyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid (PDB entry 8CCB)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2092
R free: 0.2358
Average B factor: 24.522
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate
Matthews coefficient: 2.78
Solvent content (%): 55.74
Ligand: 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-(5-chloranylthiophen-2-yl)-2-cyclohexyl-ethanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid (U83)
Ligand formula: C37 H44 Cl N O8 S
Ligand molecular weight: 698.265
Ligand SMILES: COc1ccc(cc1OC)CCC(c2cccc(c2)OCC(=O)O)OC(=O)C3CCCCN3C(=O)C(c4ccc(s4)Cl)C5CCCCC5
Ligand InChI: InChI=1S/C37H44ClNO8S/c1-44-30-17-15-24(21-31(30)45-2)14-16-29(26-11-8-12-27(22-26)46-23-34(40)41)47-37(43)28-13-6-7-20-39(28)36(42)35(25-9-4-3-5-10-25)32-18-19-33(38)48-32/h8,11-12,15,17-19,21-22,25,28-29,35H,3-7,9-10,13-14,16,20,23H2,1-2H3,(H,40,41)/t28-,29+,35+/m0/s1
Release date: 2023-04-26
Crystal structure of the human METTL3-METTL14 complex bound to Compound 3 (ASI_M3M_138) (PDB entry 6TTV)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 580 residues
Sequence: MSDTWSSIQAHKKQLDSLRERLQRRRKQDSGHLDLRNPEAALSPTFRSDSPVPTAPTSGGPKPSTASAVPELATDPELEKKLLHHLSDLALTLPTDAVSICLAISTPDAPATQDGVESLLQKFAAQELIEVKRGLLQDDAHPTLVTYADHSKLSAMMGAVAEKKGPGEVAGTVTGQKRRAEQDSTTVAAFASSLVSGLNSSASEPAKEPAKKSRKHAASDVDLEIESLLNQQSTKEQQSKKVSQEILELLNTTTAKEQSIVEKFRSRGRAQVQEFCDYGTKEECMKASDADRPCRKLHFRRIINKHTDESLGDCSFLNTCFHMDTCKYVHYEIDACMDSEAPGSKDHTPSQELALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.1976
R free: 0.2439
Average B factor: 45.93
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 25% PEG 3350, 200 mM Magnesium acetate
Ligand: (2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolane-2-carboxamide (NWW)
Ligand formula: C10 H12 N6 O4
Ligand molecular weight: 280.24
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)C(=O)N)O)O)N
Ligand InChI: InChI=1S/C10H12N6O4/c11-7-3-9(14-1-13-7)16(2-15-3)10-5(18)4(17)6(20-10)8(12)19/h1-2,4-6,10,17-18H,(H2,12,19)(H2,11,13,14)/t4-,5+,6-,10+/m0/s1
Release date: 2020-03-04
DesGla-XaS195A Bound to Aptamer 11F7t and Rivaroxaban (PDB entry 5VOF)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.6
Sequence length: 233 residues
Sequence: IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDAGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.22014
R free: 0.2533
Average B factor: 57.44
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Bicine, 0.1 M Tris base, 0.1 M Carboxylic acids, 10% PEG 20,000, 20% PEG 500 MME
Matthews coefficient: 3.28
Solvent content (%): 62.5
Ligand: 5-chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide (RIV)
Ligand formula: C19 H18 Cl N3 O5 S
Ligand molecular weight: 435.881
Ligand SMILES: c1cc(ccc1N2CCOCC2=O)N3CC(OC3=O)CNC(=O)c4ccc(s4)Cl
Ligand InChI: InChI=1S/C19H18ClN3O5S/c20-16-6-5-15(29-16)18(25)21-9-14-10-23(19(26)28-14)13-3-1-12(2-4-13)22-7-8-27-11-17(22)24/h1-6,14H,7-11H2,(H,21,25)/t14-/m0/s1
Release date: 2018-06-13
Crystal structure of human SDHA-SDHAF2 assembly intermediate (PDB entry 6VAX)
Macromolecule: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.1
Sequence length: 632 residues
Sequence: MRGSHHHHHHGSAKVSDSISAQYPVVDHEFDAVVVGAGGAGLRAAFGLSEAGFNTACVTKLFPTRSHTVAAQGGINAALGNMEEDNWRWHFYDTVKGSDWLGDQDAIHYMTEQAPAAVVELENYGMPFSRTEDGKIYQRAFGGQSLKFGKGGQAHRCCCVADRTGHSLLHTLYGRSLRYDTSYFVEYFALDLLMENGECRGVIALCIEDGSIHRIRAKNTVVATGGYGRTYFSCTSAHTSTGDGTAMITRAGLPCQDLEFVQFHPTGIYGAGCLITEGCRGEGGILINSQGERFMERYAPVAKDLASRDVVSRSMTLEIREGRGCGPEKDHVYLQLHHLPPEQLATRLPGISETAMIFAGVDVTKEPIPVLPTVHYNMGGIPTNYKGQVLRHVNGQDQIVPGLYACGEAACASVHGANRLGANSLLDLVVFGRACALSIEESCRPGDKVPPIKPNAGEESVMNLDKLRFADGSIRTSELRLSMQKSMQNHAAVFRVGSVLQEGCGKISKLYGDLKHLKTFDRGMVWNTDLVETLELQNLMLCALQTIYGAEARKESRGAHAREDYKVRIDEYDYSKPIQGQQKKPFEEHWRKHTLSYVDVGTGKVTLEYRPVIDKTLNEADCATVPPAIRSY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.59
R work: 0.1991
R free: 0.2489
Average B factor: 93.32
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 298
Crystal growth procedure: 100 mM Sodium malonate, 12 % w/v PEG 3350, 10 mM Oxaloacetate
Matthews coefficient: 2.67
Solvent content (%): 53.87
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
Release date: 2020-08-26
LINE-1 retrotransposon endonuclease domain complex with Mn2+ (PDB entry 8SP5)
Macromolecule: LINE-1 retrotransposon endonuclease
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.49
Sequence length: 239 residues
Sequence: MTGSTSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELRI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.203
R free: 0.25
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.14 M ammonium sulfate, 24% polyethylene glycol 5000 monomethyl ether, 5 mM magnesium chloride
Matthews coefficient: 2.27
Solvent content (%): 45.78
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: 2024-05-22
Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 10 (PDB entry 5JGB)
Macromolecule: TAK1 kinase - TAB1 chimera fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 315 residues
Sequence: GPLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2006
R free: 0.2437
Average B factor: 48.586
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.7M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant
Matthews coefficient: 3.99
Solvent content (%): 69.18
Ligand: N-(2-methoxy-4-{[3-(4-methylpiperazin-1-yl)propyl]carbamoyl}phenyl)-4-oxo-3,4-dihydrothieno[3,2-d]pyrimidine-7-carboxamide (6JV)
Ligand formula: C23 H28 N6 O4 S
Ligand molecular weight: 484.571
Ligand SMILES: CN1CCN(CC1)CCCNC(=O)c2ccc(c(c2)OC)NC(=O)c3csc4c3N=CNC4=O
Ligand InChI: InChI=1S/C23H28N6O4S/c1-28-8-10-29(11-9-28)7-3-6-24-21(30)15-4-5-17(18(12-15)33-2)27-22(31)16-13-34-20-19(16)25-14-26-23(20)32/h4-5,12-14H,3,6-11H2,1-2H3,(H,24,30)(H,27,31)(H,25,26,32)
Release date: 2016-07-27
Ortho-substituted phenyl sulfonyl fluoride and fluorosulfate as potent elastase inhibitory fragments (PDB entry 6E69)
Macromolecule: Neutrophil elastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.37
Sequence length: 218 residues
Sequence: IVGGRRARPHAWPFMVSLQLRGGHFCGATLIAPNFVMSAAHCVANVNVRAVRVVLGAHNLSRREPTRQVFAVQRIFENGYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLAMGWGLLGRNRGIASVLQELNVTVVTSLCRRSNVCTLVRGRQAGVCFGDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQFVNWIDSIIQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.193
R free: 0.241
Average B factor: 39.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 295
Crystal growth procedure: 0.3 M ammonium citrate, pH 5.0, 14% w/v PEG3350
Matthews coefficient: 2.94
Solvent content (%): 58.15
Ligand: 2-(fluorosulfonyl)benzene-1-sulfonic acid (HVP)
Ligand formula: C6 H5 F O5 S2
Ligand molecular weight: 240.229
Ligand SMILES: c1ccc(c(c1)S(=O)(=O)O)S(=O)(=O)F
Ligand InChI: InChI=1S/C6H5FO5S2/c7-13(8,9)5-3-1-2-4-6(5)14(10,11)12/h1-4H,(H,10,11,12)
Release date: 2019-07-24
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOOA000611a (PDB entry 7FQQ)
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): 1.88
R work: 0.17
R free: 0.2043
Average B factor: 42.047
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.29
Solvent content (%): 62.64
Ligand: (1R,3R,4S)-3-(methoxymethyl)-2-(methylsulfonyl)-2-azabicyclo[2.2.2]octan-4-ol (JKJ)
Ligand formula: C10 H19 N O4 S
Ligand molecular weight: 249.327
Ligand SMILES: COCC1C2(CCC(N1S(=O)(=O)C)CC2)O
Ligand InChI: InChI=1S/C10H19NO4S/c1-15-7-9-10(12)5-3-8(4-6-10)11(9)16(2,13)14/h8-9,12H,3-7H2,1-2H3/t8-,9-,10-/m1/s1
Release date: 2022-11-23
Crystal structure of human MTH1(G2K/D120N mutant) in complex with 2-oxo-dATP (PDB entry 5GHN)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 156 residues
Sequence: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDNSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.391
R work: 0.1487
R free: 0.1889
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: Sodium citrate, Tris, NaCl
Matthews coefficient: 1.87
Solvent content (%): 34.05
Ligand: [[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (6U4)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: C1C(C(OC1N2C=NC3=C(NC(=O)N=C32)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-7-9(14-10(17)13-8)15(3-12-7)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
Release date: 2017-01-04
Crystal structure of human protein kinase CK2alpha (CSNK2A1 gene product) in complex with the ATP-competitive inhibitor 5,6,7-tribromo-1H-triazolo[4,5-b]pyridine (PDB entry 7A4C)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.502
R work: 0.2062
R free: 0.2323
Average B factor: 45.89
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 1 MIKROLITER OF THE CK2ALPHA/INHIBITOR MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR INHIBITOR, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 1 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 25 % PEG3350, 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS BUFFER, PH 5.5) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST THE RESERVOIR SOLUTION.
Matthews coefficient: 3.22
Solvent content (%): 61.83
Ligand: 5,6,7-tris(bromanyl)-1~{H}-[1,2,3]triazolo[4,5-b]pyridine (QWW)
Ligand formula: C5 H Br3 N4
Ligand molecular weight: 356.8
Ligand SMILES: c12c(c(c(nc1nn[nH]2)Br)Br)Br
Ligand InChI: InChI=1S/C5HBr3N4/c6-1-2(7)4(8)9-5-3(1)10-12-11-5/h(H,9,10,11,12)
Release date: 2020-12-09
The SH3 domain of MLK3 in complex with poly-proline peptide derived from Htt (PDB entry 6CQ7)
Macromolecule: Mitogen-activated protein kinase kinase kinase 11, Huntingtin fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 80 residues
Sequence: GSHMYANPVWTALFDYEPSGQDELALRKGDRVEVLSRDAAISGDEGWWAGQVGGQVGIFPSNYVSRGGGPPPPGPAVAEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.19625
R free: 0.25977
Average B factor: 60.496
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.5 M Ammonium Sulphate
0.1 M Sodium Citrate pH 5.6
1.1 M Lithium Sulphate
Matthews coefficient: 4.35
Solvent content (%): 71.74
Release date: 2018-09-19
Human Carbonic Anhydrase II in complex with fluorinated benzenesulfonamide (PDB entry 6RRI)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.097
R work: 0.1193
R free: 0.1393
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate 2.7 M, TRIS 0.1 M, saturated with para-Chloromercuribenzoic acid
Matthews coefficient: 2.06
Solvent content (%): 40.23
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: 2020-04-15
Nucleotide-binding domain 1 of the human cystic fibrosis transmembrane conductance regulator (CFTR) with dATP (PDB entry 5TGK)
Macromolecule: Cystic fibrosis transmembrane conductance regulator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.49
Sequence length: 229 residues
Sequence: SLTTTEVVMENVTAFWEEGGTPVLKDINFKIERGQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKHSGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQRARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILHEGSSYFYGTFSELQNLQPDFSSKLMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.912
R work: 0.1546
R free: 0.1978
Crystallization method: MICROBATCH
Crystallization pH: 7.5
Crystallization temperature (K): 279
Crystal growth procedure: Protein buffer: 150 mM NaCl, 10% (v/v) glycerol,10% (v/v) Ethylene glycol, 10mM MgCl2, 1 mM TCEP, and 20 mM Na-HEPES, pH 7.5. Precipitant buffer: 40% (v/v) PEG 400, 100 mM NH4Cl, and 100 mM MES, pH 6
Matthews coefficient: 2.37
Solvent content (%): 48.02
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: 2018-05-09
Cathepsin B in complex with DARPin 81 (PDB entry 5MBL)
Macromolecule: Cathepsin B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.1
Sequence length: 256 residues
Sequence: LKLPASFDAREQWPQCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHTNAHVSVEVSAEDLLTCCGSMCGDGCNGGYPAEAWNFWTRKGLVSGGLYESHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKICEPGYSPTYKQDKHYGYNSYSVSNSEKDIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVTGEMMGGHAIRILGWGVENGTPYWLVANSWNTDWGDNGFFKILRGQDHCGIESEVVAGIPRTD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.81
R work: 0.1697
R free: 0.1931
Average B factor: 31.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 292
Crystal growth procedure: buffer:
50mM Tris/HCl, 300mM NaCl, 0.05% Tween-20
precipitant:
0.1M MES, 1.8M NH4SO4
Matthews coefficient: 2.87
Solvent content (%): 57.13
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: 2017-12-20
Crystal Structure of KDM4D with tetrazole ligand GF057 (PDB entry 6F5T)
Macromolecule: Lysine-specific demethylase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: AQNPNCNIMIFHPTKEEFNDFDKYIAYMESQGAHRAGLAKIIPPKEWKARETYDNISEILIATPLQQVASGRAGVFTQYHKKKKAMTVGEYRHLANSKKYQTPPHQNFEDLERKYWKNRIYNSPIYGADISGSLFDENTKQWNLGHLGTIQDLLEKECGVVIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHLGEPKTWYVVPPEHGQRLERLARELFPGSSRGCGAFLRHKVALISPTVLKENGIPFNRITQEAGEFMVTFPYGYHAGFNHGFNCAEAINFATPRWIDYGKMASQCSCGEARVTFSMDAFVRILQPERYDLWKRGQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.1784
R free: 0.1982
Average B factor: 31.8763
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 100mM HEPES, 180mM ammonium sulphate, 24% PEG 3350
Matthews coefficient: 2.6
Solvent content (%): 52.73
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: 2018-12-12
Crystal structure of CK2a2 complexed with AG1112 (PDB entry 7XYH)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 339 residues
Sequence: GPLGSMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.231
R free: 0.2822
Average B factor: 47.23
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: PEG 10000, Tris-HCl pH 8.0, Sucrose
Matthews coefficient: 2.46
Solvent content (%): 50.07
Ligand: 5-azanyl-3-[(~{Z})-1-cyano-2-(1~{H}-indol-3-yl)ethenyl]-1~{H}-pyrazole-4-carbonitrile (8BH)
Ligand formula: C15 H10 N6
Ligand molecular weight: 274.28
Ligand SMILES: c1ccc2c(c1)c(c[nH]2)C=C(C#N)c3c(c([nH]n3)N)C#N
Ligand InChI: InChI=1S/C15H10N6/c16-6-9(14-12(7-17)15(18)21-20-14)5-10-8-19-13-4-2-1-3-11(10)13/h1-5,8,19H,(H3,18,20,21)/b9-5+
Release date: 2023-01-18
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001 (PDB entry 5LBO)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 364 residues
Sequence: GSHMIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.17365
R free: 0.20965
Average B factor: 45.341
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES
Matthews coefficient: 2.63
Solvent content (%): 53.19
Ligand: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTT)
Ligand formula: C4 H10 O2 S2
Ligand molecular weight: 154.251
Ligand SMILES: C(C(C(CS)O)O)S
Ligand InChI: InChI=1S/C4H10O2S2/c5-3(1-7)4(6)2-8/h3-8H,1-2H2/t3-,4-/m0/s1
Release date: 2018-03-14
CREBBP bromodomain in complex with Cpd16 (5-(7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl)-N-methyl-1H-indole-3-carboxamide) (PDB entry 6AY3)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 115 residues
Sequence: KIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.391
R work: 0.2017
R free: 0.2372
Average B factor: 18.1426
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M MgCl2, 0.1M Bis-Tris pH6.5, 22% PEG3350
Matthews coefficient: 2.28
Solvent content (%): 46.05
Ligand: 5-[7-(difluoromethyl)-6-(1-methyl-1H-pyrazol-4-yl)-3,4-dihydroquinolin-1(2H)-yl]-N-methyl-1H-indole-3-carboxamide (C3J)
Ligand formula: C24 H23 F2 N5 O
Ligand molecular weight: 435.469
Ligand SMILES: CNC(=O)c1c[nH]c2c1cc(cc2)N3CCCc4c3cc(c(c4)c5cnn(c5)C)C(F)F
Ligand InChI: InChI=1S/C24H23F2N5O/c1-27-24(32)20-12-28-21-6-5-16(9-18(20)21)31-7-3-4-14-8-17(15-11-29-30(2)13-15)19(23(25)26)10-22(14)31/h5-6,8-13,23,28H,3-4,7H2,1-2H3,(H,27,32)
Release date: 2018-02-21