satarupa22/MacromolecularLigandDB huggingface dataset:
2.05A resolution structure of the CS-b5R domains of human Ncb5or (NADP+ form) (PDB entry 6MV2)
Macromolecule: Cytochrome b5 reductase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.6.2.2
Sequence length: 367 residues
Sequence: MGHHHHHHMGPSYPSYDWFQTDSLVTIAIYTKQKDINLDSIIVDHQNDSFRAETIIKDCLYLIHIGLSHEVQEDFSVRVVESVGKIEIVLQKKENTSWDFLGHPLKNHNSLIPRKDTGLYYRKCQLISKEDVTHDTRLFCLMLPPSTHLQVPIGQHVYLKLPITGTEIVKPYTPVSGSLLSEFKEPVLPNNKYIYFLIKIYPTGLFTPELDRLQIGDFVSVSSPEGNFKISKFQELEDLFLLAAGTGFTPMVKILNYALTDIPSLRKVKLMFFNKTEDDIIWRSQLEKLAFKDKRLDVEFVLSAPISEWNGKQGHISPALLSEFLKRNLDKSKVLVCICGPVPFTEQGVRLLHDLNFSKNEIHSFTA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1742
R free: 0.2237
Average B factor: 34.7297
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 10% (w/v) PEG 6000, 0.1 M Hepes, 0.3 M NDSB-195
Matthews coefficient: 2.63
Solvent content (%): 53.19
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: 2019-07-17
DDR1, N-[[2-(2-pyridin-3-yloxyethyl)cyclohexyl]methyl]-3-(trifluoromethoxy)benzamide, 1.970A, P212121, Rfree=25.6% (PDB entry 5SB0)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.2079
R free: 0.2556
Average B factor: 45.6325
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 11.6 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed with reservoir consisting of 0.1M Sodium Citrate pH 5.5, 0.2M Sodium Acetate, 10% PEG 4000
Matthews coefficient: 2.53
Solvent content (%): 51.47
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2022-06-29
Sad phasing on nickel-substituted human carbonic anhydrase II (PDB entry 6H6S)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 259 residues
Sequence: SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.14973
R free: 0.20365
Average B factor: 16.416
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM HEPES, 2.9 M ammonium sulfate
Matthews coefficient: 2.06
Solvent content (%): 40.25
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2019-01-09
Crystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric raccoon dog ACE2 (PDB entry 8VQR)
Macromolecule: Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2
Type: Protein, polypeptide(L)
Source organism: Nyctereutes procyonoides
EC number: 3.4
Sequence length: 602 residues
Sequence: STEDLVNTFLEKFNYEAEELSYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKEQSKLAKTYPLEEIQDSTVKRQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTEPSDSWKVVCHPTAWDLGRGDFRIKMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWSPYADHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.565
R work: 0.2138
R free: 0.2642
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 100 mM Tris (pH 8-8.5), 18-22% PEG 6000, 100 mM NaCl and ethylene glycol (0.5-2%)
Matthews coefficient: 2.79
Solvent content (%): 55.85
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: 2024-05-01
Crystal structure of chimeric carbonic anhydrase VA with 3-(benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide (PDB entry 7NZU)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNTGYLFQVEFDDSQDKAVLKGGPLDGTYRLKQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDYGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLTECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.24
R work: 0.1326
R free: 0.166
Average B factor: 17.031
Crystallization method: VAPOR DIFFUSION, SITTING DROP
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
Matthews coefficient: 2.06
Solvent content (%): 40.15
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: 2022-04-13
EED in complex with PRC2 allosteric inhibitor compound 22 (MAK683) (PDB entry 7QK4)
Macromolecule: Polycomb protein EED
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 366 residues
Sequence: GKCKYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRLR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.602
R work: 0.1818
R free: 0.2057
Average B factor: 23.97
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Bis-Tris pH 6.0, 0.2 M MgCl2, 20% PEG 3350
Matthews coefficient: 2.25
Solvent content (%): 45.23
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2022-04-13
Crystal Structure of PI3Kalpha in complex with the inhibitor NVP-BYL719 (PDB entry 7PG6)
Macromolecule: Phosphatidylinositol 3-kinase regulatory subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 287 residues
Sequence: LPPKPPKPTTVANNGMNNNMSLQDAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNNKLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKEDNIEAVGKKLHEYNTQFQEKSREYDRLYEEYTRTSQEIQMKRTAIEAFNETIKIFEEQCQTQERYSKEYIEKFKREGNEKEIQRIMHNYDKLKSRISEIIDSRRRLEEDLKKQAAEYREIDKRMNSIKPDLIQLRKTRDQYLMWLTQKGVRQKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49943744477
R work: 0.187252392396
R free: 0.240324192397
Average B factor: 70
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 10% PEG 5000, 160 mM KSCN and 100 mM sodium cacodylate pH 6.5
Matthews coefficient: 2.39
Solvent content (%): 48.56
Ligand: (2S)-N~1~-{4-methyl-5-[2-(1,1,1-trifluoro-2-methylpropan-2-yl)pyridin-4-yl]-1,3-thiazol-2-yl}pyrrolidine-1,2-dicarboxamide (1LT)
Ligand formula: C19 H22 F3 N5 O2 S
Ligand molecular weight: 441.47
Ligand SMILES: Cc1c(sc(n1)NC(=O)N2CCCC2C(=O)N)c3ccnc(c3)C(C)(C)C(F)(F)F
Ligand InChI: InChI=1S/C19H22F3N5O2S/c1-10-14(11-6-7-24-13(9-11)18(2,3)19(20,21)22)30-16(25-10)26-17(29)27-8-4-5-12(27)15(23)28/h6-7,9,12H,4-5,8H2,1-3H3,(H2,23,28)(H,25,26,29)/t12-/m0/s1
Release date: 2022-08-24
Human VKOR with Chlorophacinone (PDB entry 6WV7)
Macromolecule: Vitamin K epoxide reductase, termini restrained by green fluorescent protein
Type: Protein, polypeptide(L)
Source organism: Aequorea victoria
EC number: 1.17.4.4
Sequence length: 390 residues
Sequence: MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALCDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQENSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.483
R work: 0.1997
R free: 0.2447
Average B factor: 39.7837
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 33% PEG400, 5% DMSO, 0.1 M sodium acetate, 0.1 M MES, pH 6.5
Matthews coefficient: 3
Solvent content (%): 58.98
Ligand: Chlorophacinone (UAJ)
Ligand formula: C23 H15 Cl O3
Ligand molecular weight: 374.816
Ligand SMILES: c1ccc(cc1)C(c2ccc(cc2)Cl)C(=O)C3C(=O)c4ccccc4C3=O
Ligand InChI: InChI=1S/C23H15ClO3/c24-16-12-10-15(11-13-16)19(14-6-2-1-3-7-14)23(27)20-21(25)17-8-4-5-9-18(17)22(20)26/h1-13,19-20H/t19-/m1/s1
Release date: 2020-11-11
Crystal structure of human G protein coupled receptor (PDB entry 5ZTY)
Macromolecule: G protein coupled receptor,T4 lysozyme,G protein coupled receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 500 residues
Sequence: MKTIIALSYIFCLVFAGAPPMKDYMILSGPQKTAVAVLCTLLGLLSALENVAVLYLILSSHQLRRKPSYLFIGSLALADFLASVVFACSFVNFHVFHGVDSKAVFLLKIGSVTMTFTASVGSLLLAAIDRYLCLRYPPSYKALLTRGRALVLLGIMWVLSALVSYLPLMGWTCCPRPCSELFPLIPNDYLLSWLLFIAFLFSGIIYTYGHVLWKAHQHVASNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYARMRLDVELAKTLGLVLAVLLICWFPVLALMAHSLATTLSDQVKKAFAFCSMLCLINSMVNPVIYALRSEEIRSSAHHCLAHWKKCVRGLGEFLEVLFQGPHHHHHHHHHHDYKDDDDK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.224
R free: 0.275
Average B factor: 95.84
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.2
Crystallization temperature (K): 293
Crystal growth procedure: 100mM sodium cacodylate trihydrate pH 6.2, 40% PEG400, 400mM lithium sulfate monohydrate
Matthews coefficient: 2.9
Solvent content (%): 63.03
Ligand: N-(adamantan-1-yl)-1-(5-hydroxypentyl)-4-methyl-5-phenyl-1H-pyrazole-3-carboxamide (9JU)
Ligand formula: C26 H35 N3 O2
Ligand molecular weight: 421.575
Ligand SMILES: Cc1c(n(nc1C(=O)NC23CC4CC(C2)CC(C4)C3)CCCCCO)c5ccccc5
Ligand InChI: InChI=1S/C26H35N3O2/c1-18-23(25(31)27-26-15-19-12-20(16-26)14-21(13-19)17-26)28-29(10-6-3-7-11-30)24(18)22-8-4-2-5-9-22/h2,4-5,8-9,19-21,30H,3,6-7,10-17H2,1H3,(H,27,31)/t19-,20+,21-,26-
Release date: 2019-01-30
Crystal structure of a HER2-Nb complex (PDB entry 5MY6)
Macromolecule: Receptor tyrosine-protein kinase erbB-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 622 residues
Sequence: QVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.246
R work: 0.1848
R free: 0.2201
Average B factor: 49.2832
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.25
Crystallization temperature (K): 293.15
Crystal growth procedure: 100 mM HEPES pH 7.25, 10% 2-propanol, 22% PEG 4000
Matthews coefficient: 3.1
Solvent content (%): 60.33
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: 2017-08-09
Crystal structure of human MTH1(G2K/D120A mutant) in complex with 8-oxo-dGTP (PDB entry 5GHO)
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: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDASYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.191
R work: 0.149
R free: 0.1772
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: Sodium citrate, Sodium cacodylate, NaCl
Matthews coefficient: 1.88
Solvent content (%): 34.4
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: 2017-01-04
Crystal Structure of human phosphodiesterase 10 in complex with 7-[(5-methyl-4-propan-2-yloxypyridin-2-yl)methylsulfanyl]-6H-imidazo[4,5-g][1,3]benzothiazole (PDB entry 5SJ7)
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): 2.14
R work: 0.1962
R free: 0.2186
Average B factor: 42.384
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: 2.64
Solvent content (%): 53.36
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
HUMAN FGFR4 KINASE DOMAIN (447-753) IN COMPLEX WITH ROBLITINIB (PDB entry 6YI8)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 307 residues
Sequence: AGLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDRVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.13
R work: 0.196
R free: 0.231
Average B factor: 45.28
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: mixing 0.5 ul of protein solution (13 mg/ml in 50 mM HEPES pH 8.0, 100 mM NaCl, 3% glycerol, 1 mM TCEP and 2 mM roblitinib incubated for 1h on ice) with 0.5 ul of reservoir solution (13.5 % PEG 3350, 0.1 M (NH4)2SO4, 0.1 M NaAc pH 4.25)
Matthews coefficient: 2.39
Solvent content (%): 48.46
Ligand: N-[5-cyano-4-(2-methoxyethylamino)pyridin-2-yl]-7-methanoyl-6-[(4-methyl-2-oxidanylidene-piperazin-1-yl)methyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide (FGF)
Ligand formula: C25 H30 N8 O4
Ligand molecular weight: 506.557
Ligand SMILES: CN1CCN(C(=O)C1)Cc2cc3c(nc2C=O)N(CCC3)C(=O)Nc4cc(c(cn4)C#N)NCCOC
Ligand InChI: InChI=1S/C25H30N8O4/c1-31-7-8-32(23(35)15-31)14-18-10-17-4-3-6-33(24(17)29-21(18)16-34)25(36)30-22-11-20(27-5-9-37-2)19(12-26)13-28-22/h10-11,13,16H,3-9,14-15H2,1-2H3,(H2,27,28,30,36)
Release date: 2020-09-30
The PH domain of Bruton's tyrosine kinase mutant R28C (PDB entry 6TT2)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 169 residues
Sequence: AAVILESIFLKRSQQKKKTSPLNFKKCLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEKITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEELRKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILEN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.203
R free: 0.234
Average B factor: 30.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M TRIS 8.5 pH, 32.5% w/v PEG 3350, 200mM MgCl2, 500mM NaCl
Matthews coefficient: 2.08
Solvent content (%): 40.93
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: 2020-11-25
Crystal structure of human carbonic anhydrase II with 3-(3-((1-(2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-3-yl)-1H-1,2,3-triazol-4-yl)methyl)ureido)benzenesulfonamide (PDB entry 7NH6)
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): 1.28
R work: 0.1525
R free: 0.1754
Average B factor: 14.394
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, 0.1 M Tris pH 8.0
Matthews coefficient: 2.08
Solvent content (%): 40.89
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: 2022-02-23
Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: (2R,5S,11S,14S,18E)-2,11,17,17-tetramethyl-14-(propan-2-yl)-3-oxa-9,12,15,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone (compound 24) (PDB entry 6X4N)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 167 residues
Sequence: GHMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.1584
R free: 0.1805
Average B factor: 15.08
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
Matthews coefficient: 2.79
Solvent content (%): 55.96
Ligand: (2R,5S,11S,14S,18E)-2,11,17,17-tetramethyl-14-(propan-2-yl)-3-oxa-9,12,15,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone (UOD)
Ligand formula: C30 H39 N5 O5
Ligand molecular weight: 549.661
Ligand SMILES: CC1c2ccc3ccc(cc3n2)C=CC(C(=O)NC(C(=O)NC(C(=O)N4CCCC(N4)C(=O)O1)C)C(C)C)(C)C
Ligand InChI: InChI=1S/C30H39N5O5/c1-17(2)25-26(36)31-18(3)27(37)35-15-7-8-23(34-35)28(38)40-19(4)22-12-11-21-10-9-20(16-24(21)32-22)13-14-30(5,6)29(39)33-25/h9-14,16-19,23,25,34H,7-8,15H2,1-6H3,(H,31,36)(H,33,39)/b14-13+/t18-,19+,23-,25-/m0/s1
Release date: 2020-06-24
The crystal structure of human AURKA kinase domain in complex with AURKA-compound 9 (PDB entry 8JF4)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 263 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.89288354365
R work: 0.234016952431
R free: 0.299660770841
Average B factor: 70
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M lithium sulfate, 0.1 M TRIS pH 8.5, 25% w/v PEG 3350
Matthews coefficient: 2.89
Solvent content (%): 57.44
Ligand: 2-[4-[4-[bis(oxidanylidene)-$l^5-sulfanyl]oxyphenyl]carbonylpiperazin-1-yl]-6-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]-N-prop-2-ynyl-pyrimidine-4-carboxamide (C0N)
Ligand formula: C25 H25 N8 O5 S
Ligand molecular weight: 549.582
Ligand SMILES: C#CCNC(=O)c1cc(nc(n1)N2CCN(CC2)C(=O)c3ccc(cc3)O[S+](=O)=O)Nc4cc([nH]n4)C5CC5
Ligand InChI: InChI=1S/C25H24N8O5S/c1-2-9-26-23(34)20-15-21(28-22-14-19(30-31-22)16-3-4-16)29-25(27-20)33-12-10-32(11-13-33)24(35)17-5-7-18(8-6-17)38-39(36)37/h1,5-8,14-16H,3-4,9-13H2,(H2-,26,27,28,29,30,31,34)/p+1
Release date: 2024-02-14
The crystal structure of the GST-like domains complex of AIMP3-EPRS mutant C92SC105SC123S (PDB entry 5BMU)
Macromolecule: Eukaryotic translation elongation factor 1 epsilon-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 171 residues
Sequence: GHMAAAAELSLLEKSLGLSKGNKYSAQGERQIPVLQTNNGPSLTGLTTIAAHLVKQANKEYLLGSTAEEKAIVQQWLEYRVTQVDGHSSKNDIHTLLKDLNSYLEDKVYLTGYNFTLADILLYYGLHRFIVDLTVQEKEKYLNVSRWFCHIQHYPGIRQHLSSVVFIKNRL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.13801
R free: 0.16957
Average B factor: 31.298
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293.15
Crystal growth procedure: Ammonium sulfate, Sodium chloride, Tris-HCl
Matthews coefficient: 2.94
Solvent content (%): 58.18
Release date: 2015-10-21