satarupa22/MacromolecularLigandDB huggingface dataset:
Complex of tissue inhibitor of metalloproteinases-1 (TIMP-1) mutant (L34G/L133P/L151C/G154A) with matrix metalloproteinase-3 catalytic domain (MMP-3cd) (PDB entry 6N9D)
Macromolecule: Stromelysin-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.17
Sequence length: 165 residues
Sequence: FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.67
R work: 0.184
R free: 0.258
Average B factor: 55.1126
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2 M Sodium Acetate, 0.1 M Sodium Cacodylate: HCl, pH 6.5 18 % (w/v) PEG 8000
Matthews coefficient: 2.88
Solvent content (%): 57.3
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: 2019-05-15
Cyclophilin A complexed with tri-vector ligand 5. (PDB entry 6GJY)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.29
R work: 0.16371
R free: 0.18791
Average B factor: 21.798
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.74
Solvent content (%): 55.18
Ligand: ethyl 2-[[(4-aminophenyl)methyl-prop-2-ynyl-carbamoyl]amino]ethanoate (F1Z)
Ligand formula: C15 H19 N3 O3
Ligand molecular weight: 289.33
Ligand SMILES: CCOC(=O)CNC(=O)N(CC#C)Cc1ccc(cc1)N
Ligand InChI: InChI=1S/C15H19N3O3/c1-3-9-18(11-12-5-7-13(16)8-6-12)15(20)17-10-14(19)21-4-2/h1,5-8H,4,9-11,16H2,2H3,(H,17,20)
Release date: 2018-11-07
Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable TTP (PDB entry 6E3V)
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): 1.96
R work: 0.195
R free: 0.24
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: 14% TO 23% PEG3400, AND 350 MM SODIUM
 ACETATE IN 50 MM IMIDAZOLE (PH 7.5), VAPOR DIFFUSION, SITTING
 DROP, TEMPERATURE 298K
Matthews coefficient: 2.28
Solvent content (%): 45.99
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: 2019-04-03
Crystal structure of human PCAF bromodomain in complex with fragment MB360 (fragment 4) (PDB entry 5FE3)
Macromolecule: Histone acetyltransferase KAT2B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMGKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.19801
R free: 0.23693
Average B factor: 41.77
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8
Matthews coefficient: 3.4
Solvent content (%): 63.83
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2016-01-13
BTK in complex with inhibitor N-(3-{[(2,6-dimethylphenyl)methyl]amino}-7-methoxyindeno[1,2-c]pyrazol-6-yl)methanesulfonamide (PDB entry 6NFI)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 268 residues
Sequence: YGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.41
R work: 0.21674
R free: 0.24764
Average B factor: 55.476
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 31% w/v PEG5000 MME, 0.1 M MES, pH 6.5, 0.1 M ammonium sulfate
Matthews coefficient: 2.44
Solvent content (%): 49.63
Ligand: N-(3-{[(2,6-dimethylphenyl)methyl]amino}-7-methoxyindeno[1,2-c]pyrazol-6-yl)methanesulfonamide (KLP)
Ligand formula: C21 H22 N4 O3 S
Ligand molecular weight: 410.489
Ligand SMILES: Cc1cccc(c1CNC2=C3C=C4C=C(C(=CC4=C3N=N2)OC)NS(=O)(=O)C)C
Ligand InChI: InChI=1S/C21H22N4O3S/c1-12-6-5-7-13(2)17(12)11-22-21-16-8-14-9-18(25-29(4,26)27)19(28-3)10-15(14)20(16)23-24-21/h5-10,25H,11H2,1-4H3,(H,22,24)
Release date: 2019-03-13
Structure of the enzyme-product complex resulting from TDG action on a GU mismatch in the presence of excess base (PDB entry 4Z47)
Macromolecule: DNA
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 28 residues
Sequence: AGCTGTCCATCGCTCAXGTACAGAGCTG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1403
R free: 0.1953
Average B factor: 37.444
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 30% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate
Matthews coefficient: 2.44
Solvent content (%): 49.6
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2015-09-16
Human kallikrein 7 with aromatic coumarinic ester compound 2 covalently bound to H57 (PDB entry 6SHI)
Macromolecule: Kallikrein-7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.117
Sequence length: 224 residues
Sequence: IIDGAPCARGSHPWQVALLSGNQLHCGGVLVNERWVLTAAHCKMNEYTVHLGSDTLGDRRAQRIKASKSFRHPGYSTQTHVNDLMLVKLNSQARLSSMVKKVRLPSRCEPPGTTCTVSGWGTTTSPDVTFPSDLMCVDVKLISPQDCTKVYKDLLENSMLCAGIPDSKKNACNGDSGGPLVCRGTLQGLVSWGTFPCGQPNDPGVYTQVCKFTKWINDTMKKHR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.176
R free: 0.208
Average B factor: 33.78
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 2.9 M ammonium sulphate, 0.1 M HEPES, pH 8.5, 0.5- 2 % PEG 3350
Matthews coefficient: 2.65
Solvent content (%): 53.65
Ligand: TRIETHYLENE GLYCOL (PGE)
Ligand formula: C6 H14 O4
Ligand molecular weight: 150.173
Ligand SMILES: C(COCCOCCO)O
Ligand InChI: InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
Release date: 2020-05-20
Crystal structure of TTBK2 in complex with VNG1.63 (compound 32) (PDB entry 7Q90)
Macromolecule: Tau-tubulin kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 300 residues
Sequence: SMSGGGEQPDILSVGILVKERWKVLRKIGGGGFGEIYDALDMLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNDRFNYVVMQLQGRNLADLRRSQSRGTFTISTTLRLGRQILESIESIHSVGFLHRDIKPSNFAMGRFPSTCRKCYMLDFGLARQFTNSCGDVRPPRAVAGFRGTVRYASINAHRNREMGRHDDLWSLFYMLVEFVVGQLPWRKIKDKEQVGSIKERYDHRLMLKHLPPEFSIFLDHISSLDYFTKPDYQLLTSVFDNSIKTFGVIESDPFDWEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.19
R free: 0.2202
Average B factor: 21.648
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293.15
Crystal growth procedure: 1.6M Na/K phosphate pH 7, 5% Glycerol, 0.1M tris 8.0
Matthews coefficient: 2.81
Solvent content (%): 56.23
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2022-03-09
Crystal Structure of human phosphodiesterase 10 in complex with 6-[(3,6-dimethylpyridine-2-carbonyl)amino]-N-methyl-2-phenyl-3H-benzimidazole-5-carboxamide (PDB entry 5SGJ)
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): 2.66
R work: 0.1816
R free: 0.26
Average B factor: 45.452
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 (%): 53.48
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
PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-010-382-606 (PDB entry 5QQN)
Macromolecule: Ras-related C3 botulinum toxin substrate 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 178 residues
Sequence: SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.205
R free: 0.2786
Average B factor: 43.381
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1M bis-tris pH 5.5 24% PEG 3350
Matthews coefficient: 2.35
Solvent content (%): 47.56
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2019-12-18
Ternary complex crystal structure of DNA polymerase Beta with (alpha,beta)-CH2-(beta,gamma)-NH-dTTP (PDB entry 4RT2)
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): 1.92
R work: 0.1764
R free: 0.2108
Average B factor: 29.3692
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG3350, pH 7.5, vapor diffusion, temperature 291K
Matthews coefficient: 2.23
Solvent content (%): 44.73
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: 2015-07-01
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434783 (PDB entry 5RWR)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.43
R work: 0.1741
R free: 0.2003
Average B factor: 17.794
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.11
Solvent content (%): 41.83
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2020-11-11
PCSK9-Fab 7G7 complex bound to cis-1-amino-4-phenylcyclohexaneacyl-WNLK(hR)IGLLR - NH2 (PDB entry 6U2F)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 700 residues
Sequence: MGTVSSRRSWWPLPLLLLLLLLLGPAGARAQEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSREVSTTGSTSEGAVTAVAICCRSRHLAQASQELQHHHHHHHH
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.94
R work: 0.174
R free: 0.209
Average B factor: 60.57
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 4 M ammonium acetate, 0.1 M Tris, pH 8.5, 3% v/v 1,8 diaminooctane
Matthews coefficient: 3.78
Solvent content (%): 71.15
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: 2020-02-05
Nek2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 24 (PDB entry 6SGD)
Macromolecule: Serine/threonine-protein kinase Nek2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 279 residues
Sequence: MPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1977
R free: 0.2338
Average B factor: 37.47
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 50 mM Tris pH 8.5, 3% PEG 8000
Matthews coefficient: 2.71
Solvent content (%): 54.66
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-06-17
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1,5-di-methylenebisphosphonate inositol tetrakisphosphate (1,5-PCP-IP4) (PDB entry 6WOH)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 169 residues
Sequence: HHHHHHSSGVDLGTENLYFQSMMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.185
R free: 0.2161
Average B factor: 17.066
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 and 80 mM NaF in present of 2mM 1,5-PCP-IP4
Matthews coefficient: 2.19
Solvent content (%): 43.74
Ligand: {[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid) (4WZ)
Ligand formula: C8 H24 O28 P8
Ligand molecular weight: 816.049
Ligand SMILES: C(P(=O)(O)O)P(=O)(O)OC1C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)OP(=O)(CP(=O)(O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C8H24O28P8/c9-37(10,11)1-39(15,16)31-3-5(33-41(19,20)21)4(32-40(17,18)2-38(12,13)14)7(35-43(25,26)27)8(36-44(28,29)30)6(3)34-42(22,23)24/h3-8H,1-2H2,(H,15,16)(H,17,18)(H2,9,10,11)(H2,12,13,14)(H2,19,20,21)(H2,22,23,24)(H2,25,26,27)(H2,28,29,30)/t3-,4+,5-,6-,7-,8-/m0/s1
Release date: 2021-03-03
Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2117 (PDB entry 6SRH)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.25
R work: 0.1324
R free: 0.1601
Average B factor: 24.02
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 6.0 -- 1.4M ammonium sulfate -- 0.2M sodium/potassium tartrate
Matthews coefficient: 2.68
Solvent content (%): 54.14
Ligand: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine (LU8)
Ligand formula: C27 H32 N2 O3
Ligand molecular weight: 432.555
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H32N2O3/c1-18-23(21-8-6-19(7-9-21)20-10-12-29(2)13-11-20)16-28-17-24(18)22-14-25(30-3)27(32-5)26(15-22)31-4/h6-9,14-17,20H,10-13H2,1-5H3
Release date: 2019-09-18
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z111810692 (PDB entry 5RXD)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.33
R work: 0.1697
R free: 0.1908
Average B factor: 14.923
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.08
Solvent content (%): 40.98
Ligand: N-(3-chlorophenyl)-2,2,2-trifluoroacetamide (WNP)
Ligand formula: C8 H5 Cl F3 N O
Ligand molecular weight: 223.58
Ligand SMILES: c1cc(cc(c1)Cl)NC(=O)C(F)(F)F
Ligand InChI: InChI=1S/C8H5ClF3NO/c9-5-2-1-3-6(4-5)13-7(14)8(10,11)12/h1-4H,(H,13,14)
Release date: 2020-11-11
Structure of JMJD6 bound to Mono-Methyl Arginine. (PDB entry 6MEV)
Macromolecule: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 341 residues
Sequence: MNHKSKKRIREAKRSARPELKDSLDWTRHNYYESFSLSPAAVADNVERADALQLSVEEFVERYERPYKPVVLLNAQEGWSAQEKWTLERLKRKYRNQKFKCGEDNDGYSVKMKMKYYIEYMESTRDDSPLYIFDSSYGEHPKRRKLLEDYKVPKFFTDDLFQYAGEKRRPPYRWFVMGPPRSGTGIHIDPLGTSAWNALVQGHKRWCLFPTSTPRELIKVTRDEGGNQQDEAITWFNVIYPRTQLPTWPPEFKPLEILQKPGETVFVPGGWWHVVLNLDTTIAITQNFASSTNFPVVWHKTVRGRPKLSRKWYRILKQEHPELAVLADSVDLQESTGIASD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.2291
R free: 0.2872
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281.15
Crystal growth procedure: 0.1M sodium citrate pH 5.6
1.0M ammonium phosphate monobasic
Matthews coefficient: 3.33
Solvent content (%): 63.01
Ligand: 2-OXOGLUTARIC ACID (AKG)
Ligand formula: C5 H6 O5
Ligand molecular weight: 146.098
Ligand SMILES: C(CC(=O)O)C(=O)C(=O)O
Ligand InChI: InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
Release date: 2019-09-18
Crystal structure of FGFR4 kinase domain with 7v (PDB entry 7WCT)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GPLLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.106
R work: 0.1822
R free: 0.217
Average B factor: 33.3779
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 4.5), 0.2 M Li2SO4, 16-19 % PEG 3350
Matthews coefficient: 2.24
Solvent content (%): 45.05
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: 2022-03-30