satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human carbonic anhydrase isozyme XIII with 2-(Cyclooctylamino)-3,5,6-trifluoro-4-[(2-hydroxyethyl)thio]benzenesulfonamide (PDB entry 5OGJ)
Macromolecule: Carbonic anhydrase 13
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 263 residues
Sequence: MMSRLSWGYREHNGPIHWKEFFPIADGDQQSPIEIKTKEVKYDSSLRPLSIKYDPSSAKIISNSGHSFNVDFDDTENKSVLRGGPLTGSYRLRQVHLHWGSADDHGSEHIVDGVSYAAELHVVHWNSDKYPSFVEAAHEPDGLAVLGVFLQIGEPNSQLQKITDTLDSIKEKGKQTRFTNFDLLSLLPPSWDYWTYPGSLTVPPLLESVTWIVLKQPINISSQQLAKFRSLLCTAEGEAAAFLVSNHRPPQPLKGRKVRASFH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.06
R work: 0.132
R free: 0.155
Average B factor: 15.406
Crystallization method: EVAPORATION
Crystallization pH: 5
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M ammonium citrate (pH 7), 0.1M  sodium acetate (pH 4.5) and 26% PEG3350
Matthews coefficient: 2.18
Solvent content (%): 43.56
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
Crystal structure of the human METTL3-METTL14 complex bound to Compound 4 (ASI_M3M_047) (PDB entry 6TTW)
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): 2.2
R work: 0.1845
R free: 0.2285
Average B factor: 39.3
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)-~{N}-piperidin-4-yl-oxolane-2-carboxamide (NWZ)
Ligand formula: C15 H21 N7 O4
Ligand molecular weight: 363.372
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)C(=O)NC4CCNCC4)O)O)N
Ligand InChI: InChI=1S/C15H21N7O4/c16-12-8-13(19-5-18-12)22(6-20-8)15-10(24)9(23)11(26-15)14(25)21-7-1-3-17-4-2-7/h5-7,9-11,15,17,23-24H,1-4H2,(H,21,25)(H2,16,18,19)/t9-,10+,11-,15+/m0/s1
Release date: 2020-03-04
Crystal Structure of Neutrophil Elastase Inhibited by Eap4 from S. aureus (PDB entry 9ASS)
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: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1885
R free: 0.2124
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.01 M zinc sulfate heptahydrate
0.1M MES (pH 6.5)
25% (v/v) peg-550MME
Matthews coefficient: 3.14
Solvent content (%): 60.84
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: 2024-06-12
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of HAO1 in complex with FMOPL000388a (PDB entry 5QIB)
Macromolecule: Hydroxyacid oxidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.3.15
Sequence length: 369 residues
Sequence: SMLPRLICINDYEQHAKSVLPKSIYDYYRSGANDEETLADNIAAFSRWKLYPRMLRNVAETDLSTSVLGQRVSMPICVGATAMQRMAHVDGELATVRACQSLGTGMMLSSWATSSIEEVAEAGPEALRWLQLYIYKDREVTKKLVRQAEKMGYKAIFVTVDTPYLGNRLDDVRNRFKLPPQLRMKNFETSTLSFSPEENFGDDSGLAAYVAKAIDPSISWEDIKWLRRLTSLPIVAKGILRGDDAREAVKHGLNGILVSNHGARQLDGVPATIDVLPEIVEAVEGKVEVFLDGGVRKGTDVLKALALGAKAVFVGRPIVWGLAFQGEKGVQDVLEILKEEFRLAMALSGCQNVKVIDKTLVRKNPLAVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.48
R work: 0.1874
R free: 0.2086
Average B factor: 19.462
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.75
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MIB pH 5.75 - 7.0, 27.5-35% PEG1000
Matthews coefficient: 2.4
Solvent content (%): 48.83
Ligand: 5-(cyclohexylamino)pyrimidine-2,4(1H,3H)-dione (GX7)
Ligand formula: C10 H15 N3 O2
Ligand molecular weight: 209.245
Ligand SMILES: C1CCC(CC1)NC2=CNC(=O)NC2=O
Ligand InChI: InChI=1S/C10H15N3O2/c14-9-8(6-11-10(15)13-9)12-7-4-2-1-3-5-7/h6-7,12H,1-5H2,(H2,11,13,14,15)
Release date: 2018-07-18
Crystal structure of phosphorylated pT220 Casein Kinase I delta (CK1d), conformation 1 (PDB entry 7P7F)
Macromolecule: Casein kinase I isoform delta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 296 residues
Sequence: SMMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1879
R free: 0.221
Average B factor: 42.477
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.9
Crystallization temperature (K): 277.15
Crystal growth procedure: 20% PEG 3350, 0.1 M sodium sulfate, and 0.1 M citrate, pH 5.9
Matthews coefficient: 2.49
Solvent content (%): 50.51
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2022-04-13
Crystal structure of human WEE1 kinase domain in complex with RAC-IV-099, a MK1775 analogue (PDB entry 5VD8)
Macromolecule: Wee1-like protein kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: GAGSMKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALREVYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDLLLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGHVTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEIRQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.2033
R free: 0.2469
Average B factor: 49.6555
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 291
Crystal growth procedure: 5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5), 7.5 % PEG 3350, 1 mM RAC-IV-099
Matthews coefficient: 2.2
Solvent content (%): 43.98
Ligand: 6-{[3-chloro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-2-(prop-2-en-1-yl)-1,2-dihydro-3H-pyrazolo[3,4-d]pyrimidin-3-one (98M)
Ligand formula: C27 H31 Cl N8 O2
Ligand molecular weight: 535.04
Ligand SMILES: CC(C)(c1cccc(n1)N2c3c(cnc(n3)Nc4ccc(c(c4)Cl)N5CCN(CC5)C)C(=O)N2CC=C)O
Ligand InChI: InChI=1S/C27H31ClN8O2/c1-5-11-35-25(37)19-17-29-26(32-24(19)36(35)23-8-6-7-22(31-23)27(2,3)38)30-18-9-10-21(20(28)16-18)34-14-12-33(4)13-15-34/h5-10,16-17,38H,1,11-15H2,2-4H3,(H,29,30,32)
Release date: 2018-04-04
Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dC (PDB entry 5DB6)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.83
R work: 0.185
R free: 0.2659
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 14% to 23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole
Matthews coefficient: 2.35
Solvent content (%): 47.73
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2015-11-11
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQU)
Macromolecule: HEAT SHOCK COGNATE 71 KDA PROTEIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.3.51
Sequence length: 386 residues
Sequence: GPLGSMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1782
R free: 0.2014
Average B factor: 50.74
Crystallization pH: 8.5
Crystal growth procedure: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL
Matthews coefficient: 2.41
Solvent content (%): 48.97
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: 2016-10-05
Crystal structure of BTK kinase domain in complex with pirtobrutinib (PDB entry 8FLL)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 273 residues
Sequence: GMGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.498
R work: 0.185
R free: 0.2019
Average B factor: 27.54
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 31% PEG3350, 0.3 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5
Matthews coefficient: 1.98
Solvent content (%): 37.99
Ligand: pirtobrutinib (Y7W)
Ligand formula: C22 H21 F4 N5 O3
Ligand molecular weight: 479.427
Ligand SMILES: CC(C(F)(F)F)n1c(c(c(n1)c2ccc(cc2)CNC(=O)c3cc(ccc3OC)F)C(=O)N)N
Ligand InChI: InChI=1S/C22H21F4N5O3/c1-11(22(24,25)26)31-19(27)17(20(28)32)18(30-31)13-5-3-12(4-6-13)10-29-21(33)15-9-14(23)7-8-16(15)34-2/h3-9,11H,10,27H2,1-2H3,(H2,28,32)(H,29,33)/t11-/m0/s1
Release date: 2023-03-01
CRYSTAL STRUCTURE OF TYROSINE KINASE 2 JH2 (PSEUDO KINASE DOMAIN) COMPLEXED WITH BMS-066 AKA 2-METHOXY-N-({6-[3-METHYL-7-(METHYLAMINO)-3,5,8,10-TETRAAZATRICYCLO[7.3.0.0, 6]DODECA-1(9),2(6),4,7,11-PENTAEN-11-YL]PYRIDIN-2-YL}METHY L)ACETAMIDE (PDB entry 4WOV)
Macromolecule: Non-receptor tyrosine-protein kinase TYK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 317 residues
Sequence: MGSSHHHHHHSSGETVRFQGHMNLSQLSFHRVDQKEITQLSHLGQGTRTNVYEGRLRVEGSGDPEEGKMDDEDPLVPGRDRGQELRVVLKVLDPSHHDIALAFYETASLMSQVSHTHLAFVHGVCVRGPENIMVTEYVEHGPLDVWLRRERGHVPMAWKMVVAQQLASALSYLENKNLVHGNVCGRNILLARLGLAEGTSPFIKLSDPGVGLGALSREERVERIPWLAPECLPGGANSLSTAMDKWGFGATLLEICFDGEAPLQSRSPSEKEHFYQRQHRLPEPSCPQLATLTSQCLTYEPTQRPSFRTILRDLTRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1918
R free: 0.2144
Average B factor: 31.59
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 30% PEG5000 (methyl ether), 200 mM ammonium sulfate and 100 mM sodium cacodylate buffer, pH 6.5
Matthews coefficient: 1.97
Solvent content (%): 39.55
Ligand: 2-methoxy-N-({6-[1-methyl-4-(methylamino)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridin-7-yl]pyridin-2-yl}methyl)acetamide (3SM)
Ligand formula: C19 H21 N7 O2
Ligand molecular weight: 379.416
Ligand SMILES: CNc1c2c(c3cc([nH]c3n1)c4cccc(n4)CNC(=O)COC)n(cn2)C
Ligand InChI: InChI=1S/C19H21N7O2/c1-20-19-16-17(26(2)10-22-16)12-7-14(24-18(12)25-19)13-6-4-5-11(23-13)8-21-15(27)9-28-3/h4-7,10H,8-9H2,1-3H3,(H,21,27)(H2,20,24,25)
Release date: 2015-03-18
NSD1 SET domain in complex with BT3 and SAM (PDB entry 6KQQ)
Macromolecule: Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 223 residues
Sequence: NDKKPPPYKHIKVNRPIGRVQIFTADLSEIPRCNCKATDENPCGIDSECINRMLLYECHPTVCPAGGRCQNQCFSKRQYPEVEIFRTLQRGWGLRTKTDIKKGEFVNEYVGELIDEEECRARIRYAQEHDITNFYMLTLDKDRIIDAGPKGNYARFMNHCCQPNCETQKWSVNGDTRVGLFALSDIKAGTELTFNYNLECLGNGKTVCKCGAPNCSGFLGVRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1632
R free: 0.2012
Average B factor: 23.15
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 290
Crystal growth procedure: 18% PEG 8000, 100mM sodium cacodylate, pH 6.5, 200mM calcium Acetate
Matthews coefficient: 2.92
Solvent content (%): 57.81
Ligand: 2-azanyl-6-sulfanyl-1,3-benzothiazol-4-ol (DQL)
Ligand formula: C7 H6 N2 O S2
Ligand molecular weight: 198.265
Ligand SMILES: c1c(cc2c(c1O)nc(s2)N)S
Ligand InChI: InChI=1S/C7H6N2OS2/c8-7-9-6-4(10)1-3(11)2-5(6)12-7/h1-2,10-11H,(H2,8,9)
Release date: 2020-09-02
S100B-RSK1 crystal structure C (PDB entry 5CSN)
Macromolecule: Protein S100-B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 95 residues
Sequence: GSHMSELEKAMVALIDVFHQYSGREGDKHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDNDGDGECDFQEFMAFVAMVTTACHEFFEHE
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.2514
R free: 0.2785
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.1 M Hepes 7, 150 mM NaCl, 20% PEG6000
Matthews coefficient: 2.5
Solvent content (%): 50.76
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: 2015-11-11
CATHEPSIN L IN COMPLEX WITH (2S,4R)-4-(2-Chloro-4-methoxy-benzenesulfonyl)-1-[3-(5-chloro-pyridin-2-yl)-azetidine-3-carbonyl]-pyrrolidine-2-carboxylic acid (1-cyano-cyclopropyl)-amide (PDB entry 5F02)
Macromolecule: Cathepsin L1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.15
Sequence length: 220 residues
Sequence: APRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQDNGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSEDMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1432
R free: 0.19057
Average B factor: 23.742
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MAGNESIUM FORMATE, 15 % PEG 3350
Matthews coefficient: 2.08
Solvent content (%): 40.78
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: 2016-02-24
Crystal structure of CBP bromodomain liganded with UMB298 (compound 23) (PDB entry 7KPY)
Macromolecule: Histone acetyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 116 residues
Sequence: KKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.2019
R free: 0.2388
Average B factor: 26.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M Bis-Tris, pH 5.5
25% w/v Polyethylene glycol 3,350
Matthews coefficient: 2.29
Solvent content (%): 46.29
Ligand: 2-[2-(3-chloranyl-4-methoxy-phenyl)ethyl]-~{N}-cyclohexyl-7-(3,5-dimethyl-1,2-oxazol-4-yl)imidazo[1,2-a]pyridin-3-amine (WU1)
Ligand formula: C27 H31 Cl N4 O2
Ligand molecular weight: 479.014
Ligand SMILES: Cc1c(c(on1)C)c2ccn3c(c2)nc(c3NC4CCCCC4)CCc5ccc(c(c5)Cl)OC
Ligand InChI: InChI=1S/C27H31ClN4O2/c1-17-26(18(2)34-31-17)20-13-14-32-25(16-20)30-23(27(32)29-21-7-5-4-6-8-21)11-9-19-10-12-24(33-3)22(28)15-19/h10,12-16,21,29H,4-9,11H2,1-3H3
Release date: 2021-05-19
Crystal structure of chimeric carbonic anhydrase XII with inhibitor (PDB entry 4Q09)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFKVEFDDSQDKAVLKGGPLDGTYRLTQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDAGKASQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLNECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.139
R free: 0.178
Average B factor: 17.485
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Matthews coefficient: 1.97
Solvent content (%): 37.2
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: 2015-01-28
Crystal structure of human Naa50 in complex with CoA and an inhibitor (compound 4a) identified using DNA encoded library technology (PDB entry 6WFK)
Macromolecule: N-alpha-acetyltransferase 50
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.258
Sequence length: 171 residues
Sequence: GSMKGSRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAYFNDIAVGAVCCRVDHSQNQKRLYIMTLGCLAPYRRLGIGTKMLNHVLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETKKNYYKRIEPADAHVLQKNLKVPSGQNADVQKTDN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.2
R free: 0.222
Average B factor: 47.48
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 294
Crystal growth procedure: Compound 4a soaked into crystals of Naa50+CoA. CoA co-crystals: Naa50 apo protein (14.3 mg/ml) was incubated with CoA in a 1:3 molar ratio on ice for 60 min. Crystallization solution: 0.1 M Na acetate, pH5.0, 25% (w/v) PEG 3350, 10 mM Dithiothreitol (DTT), and 0.1% Dioxane
Matthews coefficient: 2.72
Solvent content (%): 54.85
Ligand: (4S)-1-methyl-N-{(3S,5S)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide (U2J)
Ligand formula: C23 H24 N10 O5 S
Ligand molecular weight: 552.566
Ligand SMILES: CNC(=O)c1csc(n1)C2CC(CN2C(=O)c3ccc(cc3)c4[nH]nnn4)NC(=O)C5CC(=O)N(C(=O)N5)C
Ligand InChI: InChI=1S/C23H24N10O5S/c1-24-19(35)15-10-39-21(26-15)16-7-13(25-20(36)14-8-17(34)32(2)23(38)27-14)9-33(16)22(37)12-5-3-11(4-6-12)18-28-30-31-29-18/h3-6,10,13-14,16H,7-9H2,1-2H3,(H,24,35)(H,25,36)(H,27,38)(H,28,29,30,31)/t13-,14-,16-/m0/s1
Release date: 2020-07-01
BTK complex with compound 7 (PDB entry 6BIK)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 287 residues
Sequence: MGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDENLYFQGEEYMPTEHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.901
R work: 0.1609
R free: 0.2224
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: PEG 10000, Li2SO4, pH 7.0
Matthews coefficient: 2.07
Solvent content (%): 40.65
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2018-11-07
The crystal structure of CK2alpha in complex with compound 4 (PDB entry 5OS7)
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: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.2208
R free: 0.2475
Average B factor: 25.53
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: 2.24
Solvent content (%): 45.05
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
Crystal Structure of human phosphodiesterase 10 in complex with 6-cyclopropyl-N-[4-(dimethylcarbamoyl)pyridin-3-yl]-3-(pyrimidin-5-ylamino)pyridine-2-carboxamide (PDB entry 5SJS)
Macromolecule: cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 343 residues
Sequence: GSSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1733
R free: 0.2536
Average B factor: 59.866
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2
Matthews coefficient: 2.61
Solvent content (%): 52.94
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: 2022-10-12