satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340 (PDB entry 4WUA)
Macromolecule: SRSF protein kinase 1, linker, SRSF protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 401 residues
Sequence: GSHMPEQEEEILGSDDDEQEDPNDYCKGGYHLVKIGDLFNGRYHVIRKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSDPNDPNREMVVQLLDDFKISGVNGTHICMVFEVLGHHLLKWIIKSNYQGLPLPCVKKIIQQVLQGLDYLHTKCRIIHTDIKPENILLSVNEQYIRRLAAEATEWQRSGAPPPSGSAVSTAPATAGNFLVNPLEPKNAEKLKVKIADLGNACWVHKHFTEDIQTRQYRSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEEYTRDEDHIALIIELLGKVPRKLIVAGKYSKEFFTKKGDLKHITKLKPWGLFEVLVEKYEWSQEEAAGFTDFLLPMLELIPEKRATAAECLRHPWLNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.19661
R free: 0.23634
Average B factor: 36.412
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium citrate, 0.2M ammonium acetate, 5%PEG6000
Matthews coefficient: 2.77
Solvent content (%): 55.64
Ligand: N-[2-(1-piperidinyl)-5-(trifluoromethyl)phenyl]-4-pyridinecarboxamide (3UL)
Ligand formula: C18 H18 F3 N3 O
Ligand molecular weight: 349.35
Ligand SMILES: c1cc(c(cc1C(F)(F)F)NC(=O)c2ccncc2)N3CCCCC3
Ligand InChI: InChI=1S/C18H18F3N3O/c19-18(20,21)14-4-5-16(24-10-2-1-3-11-24)15(12-14)23-17(25)13-6-8-22-9-7-13/h4-9,12H,1-3,10-11H2,(H,23,25)
Release date: 2015-09-16
Crystal structure of the C276S mutant of MAP2K7 (PDB entry 5Y8U)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 323 residues
Sequence: TGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLSDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPRTSGVLSQPHLPFFRHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.92
R work: 0.23011
R free: 0.2988
Average B factor: 55.161
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG3350, sodium citrate
Matthews coefficient: 2.63
Solvent content (%): 53.21
Release date: 2017-10-11
THE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH GTC000233 (PDB entry 4YJT)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 281 residues
Sequence: PEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.1743
R free: 0.2083
Average B factor: 24.51
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 30% Jeffamine ED-2001, 10% Glycerol, 0.1M MES pH6.0, 5mM TCEP
Matthews coefficient: 2.11
Solvent content (%): 41.74
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: 2015-09-30
Crystal structure of human calcineurin (PDB entry 4OR9)
Macromolecule: Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 544 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMAAPEPARAAPPPPPPPPPPPGADRVVKAVPFPPTHRLTSEEVFDLDGIPRVDVLKNHLVKEGRVDEEIALRIINEGAAILRREKTMIEVEAPITVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYVDRGYFSIECVLYLWVLKILYPSTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYEACMEAFDSLPLAALLNQQFLCVHGGLSPEIHTLDDIRRLDRFKEPPAFGPMCDLLWSDPSEDFGNEKSQEHFSHNTVRGCSYFYNYPAVCEFLQNNNLLSIIRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNVLSICSDDELMTEGEDQFDGSAAARKEIIRNKIRAIGKMARVFSVLREESESVLTLKGLTPTGMLPSGVLAGGRQTLQSATVEAIEAEKAIRGFSPPHRICSFEEAKGLDRINERMPPRKDAVQQDGFNSLNTAHATENHGTGNHTAQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.1827
R free: 0.2148
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 294
Crystal growth procedure: 100mM MES, pH 5.8, 7% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Matthews coefficient: 3.11
Solvent content (%): 60.48
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2015-05-20
Crystal structure of Protein Phosphatase 1 (PP1) bound to the muscle glycogen-targeting subunit (Gm) (PDB entry 6DNO)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 299 residues
Sequence: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPAD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1859
R free: 0.2096
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 0.4 M magnesium formate dihydrate, 0.1 M Sodium Acetate trihydrate
Matthews coefficient: 2.12
Solvent content (%): 41.95
Release date: 2019-01-23
Synthesis, carbonic anhydrase inhibition and protein X-ray structure of the unusual natural product primary sulfonamide Psammaplin C (PDB entry 5A6H)
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): 1.57
R work: 0.1454
R free: 0.1932
Average B factor: 16.18
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 281
Crystal growth procedure: EQUAL VOLUMES OF PROTEIN AND RESERVOIR (250 NL EACH) AT 8C WITH THE PROTEIN AT 7.5 MG/ML AND THE RESERVOIR BEING 2.6 M AMMONIUM SULFATE, 100 MM TRIS PH 8
Matthews coefficient: 2.11
Solvent content (%): 41.8
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: 2016-05-25
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate/ATP/Mn (PDB entry 8PPD)
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): 1.77
R work: 0.20191
R free: 0.23047
Average B factor: 39.839
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.83 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. 
Protein:precipitant ratio 1:1. 
Protein concentration: 18 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, 10 mM ligand, 3 mM ATP and 3 mM MnCl2.
Matthews coefficient: 2.69
Solvent content (%): 54.31
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: 2024-02-28
Crystal structure of human MMP-7 in complex with inhibitor (PDB entry 8JUF)
Macromolecule: Matrilysin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.23
Sequence length: 175 residues
Sequence: MGYSLFPNSPKWTSKVVTYRIVSYTRDLPHITVDRLVSKALNMWGKEIPLHFRKVVWGTADIMIGFARGAHGDSYPFDGPGNTLAHAFAPGTGLGGDAHFDEDERWTDGSSLGINFLYAATHQLGHSLGMGHSSDPNAVMYPTYGNGDPQNFKLSQDDIKGIQKLYGKRSNSRKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.1967
R free: 0.22006
Average B factor: 28.515
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10% w/v Polyethylene glycol 8000,  100mM Tris pH7.0,  200mM Magnesium chloride
Matthews coefficient: 2.33
Solvent content (%): 47.17
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: 2023-11-01
Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 18X at 1.86 A resolution (PDB entry 4ZL1)
Macromolecule: Dihydroorotate dehydrogenase (quinone), mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.3.5.2
Sequence length: 390 residues
Sequence: MGHHHHHHHHHHSSGHIDDDDKHMATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPRARFQDSDMLEVRVLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVVNVSSPNTAGLRSLQGKAELRRLLTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.15993
R free: 0.17893
Average B factor: 23.267
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.8
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M acetate, 40mM UDAO, 20.8mM N,N-dimethyldecylamine-N-oxide(DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate, 1mM inhibitor
Matthews coefficient: 3.47
Solvent content (%): 64.53
Ligand: OROTIC ACID (ORO)
Ligand formula: C5 H4 N2 O4
Ligand molecular weight: 156.096
Ligand SMILES: C1=C(NC(=O)NC1=O)C(=O)O
Ligand InChI: InChI=1S/C5H4N2O4/c8-3-1-2(4(9)10)6-5(11)7-3/h1H,(H,9,10)(H2,6,7,8,11)
Release date: 2016-05-04
Human thymine DNA glycosylase bound to DNA with 2'-F-5-carboxyl-dC substrate analog (PDB entry 6U17)
Macromolecule: G/T mismatch-specific thymine DNA glycosylase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.29
Sequence length: 227 residues
Sequence: SKKSGKSAKSKEKQEKITDTFKVKRKVDRFNGVSEAELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.189
R free: 0.224
Average B factor: 51.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: PEG3350, sodium Acetate, Ammonium acetate
Matthews coefficient: 2.35
Solvent content (%): 47.72
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: 2019-11-20
Development of N-(Functionalized benzoyl)-homocycloleucyl-glycinonitriles as Potent Cathepsin K Inhibitors. (PDB entry 4X6I)
Macromolecule: Cathepsin K
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.38
Sequence length: 215 residues
Sequence: APDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGNKGYILMARNKNNACGIANLASFPKM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.87
R work: 0.181
R free: 0.237
Average B factor: 8.629
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: Lithium sulfate 0.2M,
Sodium acetate 0.1M,
Peg 8000 30%
Matthews coefficient: 1.85
Solvent content (%): 33.65
Ligand: 2-amino-4-bromo-N-{1-[(cyanomethyl)carbamoyl]cyclohexyl}benzamide (3Y1)
Ligand formula: C16 H19 Br N4 O2
Ligand molecular weight: 379.252
Ligand SMILES: c1cc(c(cc1Br)N)C(=O)NC2(CCCCC2)C(=O)NCC#N
Ligand InChI: InChI=1S/C16H19BrN4O2/c17-11-4-5-12(13(19)10-11)14(22)21-16(6-2-1-3-7-16)15(23)20-9-8-18/h4-5,10H,1-3,6-7,9,19H2,(H,20,23)(H,21,22)
Release date: 2015-09-30
Homodimerization of Tie2 Fibronectin-like domains 1-3 in space group C2 (PDB entry 5MYA)
Macromolecule: Angiopoietin-1 receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 333 residues
Sequence: MKFLVNVALVFMVVYISYIYADPVLPKPLNAPNVIDTGHNFAVINISSEPYFGDGPIKSKKLLYKPVNHYEAWQHIQVTNEIVTLNYLEPRTEYELCVQLVRRGEGGEGHPGPVRRFTTASIGLPPPRGLNLLPKSQTTLNLTWQPIFPSSEDDFYVEVERRSVQKSDQQNIKVPGNLTSVLLNNLHPREQYVVRARVNTKAQGEWSEDLTAWTLSDILPPQPENIKISNITHSSAVISWTILDGYSISSITIRYKVQGKNEDQHVDVKIKNATITQYQLKGLEPETAYQVDIFAENNIGSSNPAFSHELVTLPESQAPADLGIEGRHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2345
R free: 0.2772
Average B factor: 139.9
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.1 M Tris buffer at pH 7.0 - 8.5 and 14-20% PEG 3350 (w/v)
Matthews coefficient: 2.7
Solvent content (%): 54
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2017-04-26
Carbonic anhydrase II in complex with activating histamine pyridinium derivative (PDB entry 5W8B)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.601
R work: 0.1559
R free: 0.1832
Average B factor: 17.085
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 296
Crystal growth procedure: 1.4M Sodium Citrate, 50mM Tris, pH 7.8
Matthews coefficient: 2.11
Solvent content (%): 41.62
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: 2018-05-30
Structure of human beta 1,3-N-acetylglucosaminyltransferase 2 iodide-derivative (PDB entry 7JHI)
Macromolecule: N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.149
Sequence length: 384 residues
Sequence: MHHHHHHHHENLYFQGSSSQEKNGKGEVIIPKEKFWKISTPPEAYWNREQEKLNRQYNPILSMLTNQTGEAGRLSNISHLNYCEPDLRVTSVVTGFNNLPDRFKDFLLYLRCRNYSLLIDQPDKCAKKPFLLLAIKSLTPHFARRQAIRESWGQESNAGNQTVVRVFLLGQTPPEDNHPDLSDMLKFESEKHQDILMWNYRDTFFNLSLKEVLFLRWVSTSCPDTEFVFKGDDDVFVNTHHILNYLNSLSKTKAKDLFIGDVIHNAGPHRDKKLKYYIPEVVYSGLYPPYAGGGGFLYSGHLALRLYHITDQVHLYPIDDVYTGMCLQKLGLVPEKHKGFRTFDIEEKNKNNICSYVDLMLVHSRKPQEMIDIWSQLQSAHLKC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2016
R free: 0.2476
Average B factor: 30.6588
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 24% PEG1500, 20% glycerol
Matthews coefficient: 2.38
Solvent content (%): 48.33
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2020-11-18
Crystal structure of the DDX41 DEAD domain in an apo open form (PDB entry 5GVS)
Macromolecule: Probable ATP-dependent RNA helicase DDX41
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.13
Sequence length: 231 residues
Sequence: ILVEGDGIPPPIKSFKEMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGGMSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRTIFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.20722
R free: 0.27487
Average B factor: 24.482
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: tri-ammonium citrate,
PEG 3350
Matthews coefficient: 2.26
Solvent content (%): 45.64
Release date: 2016-10-19
Fragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues (PDB entry 5AQN)
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): 2.45
R work: 0.1927
R free: 0.228
Average B factor: 59.37
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: 2.45
Solvent content (%): 49.83
Ligand: BENZOFURO[3,2-D]PYRIMIDIN-4(3H)-ONE (JG8)
Ligand formula: C10 H6 N2 O2
Ligand molecular weight: 186.167
Ligand SMILES: c1ccc2c(c1)c3c(o2)C(=O)NC=N3
Ligand InChI: InChI=1S/C10H6N2O2/c13-10-9-8(11-5-12-10)6-3-1-2-4-7(6)14-9/h1-5H,(H,11,12,13)
Release date: 2016-10-05
Crystal structure of human METTL1 bound to Sinefungin (PDB entry 7PL1)
Macromolecule: tRNA (guanine-N(7)-)-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.33
Sequence length: 252 residues
Sequence: MHHHHHHSSGRENLYFQGDHTLRYPVKPEEMDWSELYPEFFAPLTQNQSHDDPKDKKEKRAQAQVEFADIGCGYGGLLVELSPLFPDTLILGLEIRVKVSDYVQDRIRALRAAPAGGFQNIACLRSNAMKHLPNFFYKGQLTKMFFLFPDPHFKRTKHKWRIISPTLLAEYAYVLRVGGLVYTITDVLELHDWMCTHFEEHPLFERVPLEDLSEDPVVGHLGTSTEEGKKVLRNGGKNFPAIFRRIQDPVLQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1896
R free: 0.2121
Average B factor: 31.31
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 200 mM lithium sulfate, 20% PEG 1000, 100 mM phosphate-citrate buffer pH 4.2
Matthews coefficient: 2.8
Solvent content (%): 56.08
Ligand: SINEFUNGIN (SFG)
Ligand formula: C15 H23 N7 O5
Ligand molecular weight: 381.387
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
Ligand InChI: InChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
Release date: 2021-09-15
Crystal structure of COQ8A-CA157 inhibitor complex in space group C2 (PDB entry 7UDP)
Macromolecule: Atypical kinase COQ8A, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7
Sequence length: 393 residues
Sequence: SSEANAERIVRTLCKVRGAALKLGQMLSIQDDAFINPHLAKIFERVRQSADFMPLKQMMKTLNNDLGPNWRDKLEYFEERPFAAASIGQVHLARMKGGREVAMKIQYPGVAQSINSDVNNLMAVLNMSNMLPEGLFPEHLIDVLRRELALECDYQREAACARKFRDLLKGHPFFYVPEIVDELCSPHVLTTELVSGFPLDQAEGLSQEIRNEICYNILVLCLRELFEFHFMQTDPNWSNFFYDPQQHKVALLDFGATREYDRSFTDLYIQIIRAAADRDRETVRAKSIEMKFLTGYEVKVMEDAHLDAILILGEAFASDEPFDFGTQSTTEKIHNLIPVMLRHRLVPPPEETYSLHRKMGGSFLICSKLKARFPCKAMFEEAYSNYCKRQAQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.01
R work: 0.2397
R free: 0.2794
Average B factor: 97.6354
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: Crystals were grown in a MRC SD2 plate set by a STP Labtech Mosquito. Protein at 17.89 mg/ml (390 uM) and 500 uM CA157 were inc for 30 min at ambient temp prior to setting the plate.  The droplet providing the crystal used for data collection and refinement was  200 nL of protein-CA157 solution and 25 nL reservoir,  0.65 M sodium succinate pH 7, 0.1M HEPPS buffer, pH 8.0.
Matthews coefficient: 2.27
Solvent content (%): 45.78
Ligand: 4-[(3,4,5-trimethoxyphenyl)amino]quinoline-7-carbonitrile (MVS)
Ligand formula: C19 H17 N3 O3
Ligand molecular weight: 335.357
Ligand SMILES: COc1cc(cc(c1OC)OC)Nc2ccnc3c2ccc(c3)C#N
Ligand InChI: InChI=1S/C19H17N3O3/c1-23-17-9-13(10-18(24-2)19(17)25-3)22-15-6-7-21-16-8-12(11-20)4-5-14(15)16/h4-10H,1-3H3,(H,21,22)
Release date: 2023-01-18
Crystal structure of human DNA polymerase eta incorporating dITP across dC (PDB entry 8FN3)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 432 residues
Sequence: MATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.2073
R free: 0.2531
Average B factor: 43.52
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, pH 6.5, 20% PEG2000 MME, 5 mM calcium chloride
Matthews coefficient: 2.1
Solvent content (%): 41.42
Ligand: 2'-deoxyinosine 5'-triphosphate (Y43)
Ligand formula: C10 H15 N4 O13 P3
Ligand molecular weight: 492.166
Ligand SMILES: c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)NC=NC2=O
Ligand InChI: InChI=1S/C10H15N4O13P3/c15-5-1-7(14-4-13-8-9(14)11-3-12-10(8)16)25-6(5)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,15H,1-2H2,(H,20,21)(H,22,23)(H,11,12,16)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2023-05-03