satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of PDE4D catalytic domain complexed with compound 18d (PDB entry 7F2M)
Macromolecule: Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 507 residues
Sequence: MASNKFKRMLNRELTHLSEMSRSGNQVSEFISNTFLDKQHEVEIPSPTQKEKEKKKRPMSQISGVKKLMHSSSLTNSSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTLEEDGESDTEKDSGSQVEEDTSCSDSKTLCTQDSESTEIPLDEQVEEEAVGEEEESQPEACVIDDRSPDT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.20004160481
R work: 0.197984745252
R free: 0.246751805764
Average B factor: 25.7586682878
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M HEPES (pH 7.4), 0.1 M MgCl2, 15% PEG3350, 10% isopropanol, and 25% ethylene glycol
Matthews coefficient: 1.62
Solvent content (%): 24.1
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: 2021-10-20
Crystal structure of human Heme Oxygenase-2 in complex with Laurate (PDB entry 5UCA)
Macromolecule: Heme oxygenase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.18
Sequence length: 226 residues
Sequence: MGSSHHHHHHSSGMADLSELLKEGTKEAHDRAENTQFVKDFLKGNIKKELFKLATTALYFTYSALEEEMERNKDHPAFAPLYFPMELHRKEALTKDMEYFFGENWEEQVQCPKAAQKYVERIHYIGQNEPELLVAHAYTRYMGDLSGGQVLKKVAQRALKLPSTGEGTQFYLFENVDNAQQFKQLYRARMNALDLNMKTKERIVEEANKAFEYNMQIFNELDQAGS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.117
R work: 0.1933
R free: 0.2492
Average B factor: 40.7213
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Bis-Tris (pH 6.5) and 24% (w/v) PEG 2000 monomethyl ether
Matthews coefficient: 2.13
Solvent content (%): 42.38
Ligand: LAURIC ACID (DAO)
Ligand formula: C12 H24 O2
Ligand molecular weight: 200.318
Ligand SMILES: CCCCCCCCCCCC(=O)O
Ligand InChI: InChI=1S/C12H24O2/c1-2-3-4-5-6-7-8-9-10-11-12(13)14/h2-11H2,1H3,(H,13,14)
Release date: 2017-02-15
Myotubularin-related protein 2 (PDB entry 5GNH)
Macromolecule: Myotubularin-related protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.95
Sequence length: 571 residues
Sequence: MEEPPLLPGENIKDMAKDVTYICPFTGAVRGTLTVTNYRLYFKSMERDPPFVLDASLGVINRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKPEGRTRRSIFENLMKYAFPVSNNLPLFAFEYKEVFPENGWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHSSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNPRMKPQEPIHNRYKELLAKRAELQKKVEELQREISNRSTSSSERASSPAQCVTPVQTVV
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.20295
R free: 0.2576
Average B factor: 53.843
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 100mM HEPES pH 7.5, 10% (v/v) polyethylene glycol 6000
Matthews coefficient: 2.2
Solvent content (%): 44.08
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: 2017-07-26
Rapid Discovery of Pyrido[3,4-d]pyrimidine Inhibitors of Monopolar Spindle kinase 1 (MPS1) Using a Structure-Based Hydridization Approach (PDB entry 5EHY)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.26
R work: 0.1854
R free: 0.2072
Average B factor: 73.41
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1m HEPES pH 7.5
30-45% PEG300
Matthews coefficient: 3.11
Solvent content (%): 60.42
Ligand: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL (7PE)
Ligand formula: C14 H30 O7
Ligand molecular weight: 310.384
Ligand SMILES: CCOCCOCCOCCOCCOCCOCCO
Ligand InChI: InChI=1S/C14H30O7/c1-2-16-5-6-18-9-10-20-13-14-21-12-11-19-8-7-17-4-3-15/h15H,2-14H2,1H3
Release date: 2016-04-20
Crystal Structure of PAK4 in complex with inhibitor CZH062 (PDB entry 5XVF)
Macromolecule: Serine/threonine-protein kinase PAK 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 290 residues
Sequence: SSHEQFRAALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.655
R work: 0.1935
R free: 0.2514
Average B factor: 74.48
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M HEPES pH 7.5, 25% PEG3350.
Matthews coefficient: 2.96
Solvent content (%): 58.47
Ligand: 2-(4-azanylpiperidin-1-yl)-6-chloranyl-N-(1-methylimidazol-4-yl)quinazolin-4-amine (8FR)
Ligand formula: C17 H20 Cl N7
Ligand molecular weight: 357.841
Ligand SMILES: Cn1cc(nc1)Nc2c3cc(ccc3nc(n2)N4CCC(CC4)N)Cl
Ligand InChI: InChI=1S/C17H20ClN7/c1-24-9-15(20-10-24)22-16-13-8-11(18)2-3-14(13)21-17(23-16)25-6-4-12(19)5-7-25/h2-3,8-10,12H,4-7,19H2,1H3,(H,21,22,23)
Release date: 2018-02-07
Crystal Structure of ERK2 in complex with 7-(1-benzyl-1H-pyrazol-4-yl)-2-(pyridin-4-yl)-5H-pyrrolo[2,3-b]pyrazine (PDB entry 4QPA)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 369 residues
Sequence: MGSHHHHHHMAAAAAAGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.2118
R free: 0.2526
Matthews coefficient: 2.77
Solvent content (%): 55.54
Ligand: 7-(1-benzyl-1H-pyrazol-4-yl)-2-(pyridin-4-yl)-5H-pyrrolo[2,3-b]pyrazine (35W)
Ligand formula: C21 H16 N6
Ligand molecular weight: 352.392
Ligand SMILES: c1ccc(cc1)Cn2cc(cn2)c3c[nH]c4c3nc(cn4)c5ccncc5
Ligand InChI: InChI=1S/C21H16N6/c1-2-4-15(5-3-1)13-27-14-17(10-25-27)18-11-23-21-20(18)26-19(12-24-21)16-6-8-22-9-7-16/h1-12,14H,13H2,(H,23,24)
Release date: 2015-09-23
JAK1 complexed with compound 28 (PDB entry 5WO4)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 302 residues
Sequence: GDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1865
R free: 0.2108
Average B factor: 35.14
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES pH 6.0, 30% (w/v) PEG 6000
Matthews coefficient: 2.33
Solvent content (%): 47.3
Ligand: 3-[(4-chloro-3-methoxyphenyl)amino]-1-[(3R,4S)-4-cyanooxan-3-yl]-1H-pyrazole-4-carboxamide (B7V)
Ligand formula: C17 H18 Cl N5 O3
Ligand molecular weight: 375.81
Ligand SMILES: COc1cc(ccc1Cl)Nc2c(cn(n2)C3COCCC3C#N)C(=O)N
Ligand InChI: InChI=1S/C17H18ClN5O3/c1-25-15-6-11(2-3-13(15)18)21-17-12(16(20)24)8-23(22-17)14-9-26-5-4-10(14)7-19/h2-3,6,8,10,14H,4-5,9H2,1H3,(H2,20,24)(H,21,22)/t10-,14+/m1/s1
Release date: 2017-12-06
Crystal Structure of human phosphodiesterase 10 in complex with 1-methyl-6-[2-(1-methyl-4-phenylimidazol-2-yl)ethyl]-5H-pyrazolo[3,4-d]pyrimidin-4-one (PDB entry 5SJ4)
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): 2.77
R work: 0.1952
R free: 0.2779
Average B factor: 63.001
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: 2.63
Solvent content (%): 53.21
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
Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with Fasudil (M77) (PDB entry 5LCP)
Macromolecule: cAMP-dependent protein kinase catalytic subunit alpha
Type: Protein, polypeptide(L)
Source organism: Cricetulus griseus
EC number: 2.7.11.11
Sequence length: 353 residues
Sequence: GHMGNAAAAKKGSEQESVKEFLAKAKEEFLKKWESPSQNTAQLDHFDRIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFTEF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.433
R work: 0.1327
R free: 0.1659
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 277.15
Crystal growth procedure: Drop:
10 mg/ml PKA (0.240 mM)
30 mM MBT (MES/Bis-Tris Puffer pH 6.9)
1 mM DTT
0.1 mM EDTA
75 mM LiCl
0.03 mM Mega 8
0.07mM PKI (Sigma: P7739)
1.2 mM ligand solved in DMSO (50 mM Stock)

Reservoir: 18% Methanol

0.003 mL drop volume, 0.4 mL reservoir volume
Matthews coefficient: 2.15
Solvent content (%): 54.12
Ligand: 5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE (M77)
Ligand formula: C14 H17 N3 O2 S
Ligand molecular weight: 291.369
Ligand SMILES: c1cc2cnccc2c(c1)S(=O)(=O)N3CCCNCC3
Ligand InChI: InChI=1S/C14H17N3O2S/c18-20(19,17-9-2-6-15-8-10-17)14-4-1-3-12-11-16-7-5-13(12)14/h1,3-5,7,11,15H,2,6,8-10H2
Release date: 2018-01-17
Human DNA polymerase eta extension complex with cdA at the -2 position (PDB entry 6M7P)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1812
R free: 0.2176
Average B factor: 29.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 16 % PEG 2000 MME
100 mM MES, pH 6.0
Matthews coefficient: 2.09
Solvent content (%): 41.22
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine (DZ4)
Ligand formula: C10 H17 N6 O11 P3
Ligand molecular weight: 490.197
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1
Release date: 2018-09-12
Functional construct of the Eukaryotic elongation factor 2 kinase bound to Calmodulin, ADP and to the A-484954 inhibitor and showing two conformations for the 498-520 loop (PDB entry 8GM5)
Macromolecule: Eukaryotic elongation factor 2 kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.20
Sequence length: 531 residues
Sequence: SSSGSPANSFHFKEAWKHAIQKAKHMPDPWAEFHLEDIATERATRHRYNAVTGEWLDDEVLIKMASQPFGRGAMRECFRTKKLSNFLHAQQWKGASNYVAKRYIEPVDRDVYFEDVRLQMEAKLWGEEYNRHKPPKQVDIMQMCIIELKDRPGKPLFHLEHYIEGKYIKYNSNSGFVRDDNIRLTPQAFSHFTFERSGHQLIVVDIQGVGDLYTDPQIHTETGTDFGDGNLGVRGMALFFYSHACNRICESMGLAPFDLSPRERDAVNQNTKLLQSAKTILRGTEEKCGGGGGGGNSSRLHLPRASAVALEVQRLNALDLEKKIGKSILGKVHLAMVRYHEGGRFCEKGEEWDQESAVFHLEHAANLGELEAIVGLGLMYSQLPHHILADVSLKETEENKTKGFDYLLKAAEAGDRQSMILVARAFDSGQNLSPDRCQDWLEALHWYNTALEMTDCDEGGEYDGMQDEPRYMMLAREAEMLFTGGYGLEKDPQRSGDLYTQAAEAAMEAMKGRLANQYYQKAEEAWAQMEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.181
R free: 0.225
Average B factor: 42.27
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.5
Crystallization temperature (K): 295.15
Crystal growth procedure: Cocktail:16.55% PEG-3350, 0.2 M NaF, 100 mM BisTris-Propane
Protein solution: 10.3 mg/mL 20 mM Tris pH 7.5, 100 mM NaCl, 3 mM CaCl2, 1mM TCEP, 1.5 m Inhibitor , 3.1 % DMSO
2protein/1cocktail (0.2 ul total)
Matthews coefficient: 2.68
Solvent content (%): 53.71
Ligand: ADENOSINE-5'-DIPHOSPHATE (ADP)
Ligand formula: C10 H15 N5 O10 P2
Ligand molecular weight: 427.201
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2023-05-31
Crystal structure of a double mutant catalytic domain of Human MMP12 in complex with an hydroxamate analogue of RXP470 (PDB entry 5D3C)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYAYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.314
R work: 0.1526
R free: 0.1913
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 293
Crystal growth procedure: Protein : MMP12 F67D K241A, 1 mili-M + 10 mili-M AHA
Drop : 1 micro-L protein + 0.2 micro-L inhibitor (5 mili-M in DMSO)
Precipitant : 20% PEG4000, 0.2 M TRIS pH 9.5
Cryoprotectant : 10 % diethylene glycol + 5 % glycerol + 10 % 2,3-butanediol + 5 % 1,4-dioxane +25% PEG6000,+ 100 mili-M TRIS HCl, pH 8.
Matthews coefficient: 2.25
Solvent content (%): 45.38
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: 2016-08-17
Structure of CHK1 12-pt. mutant complex with arylbenzamide LRRK2 inhibitor (PDB entry 5OQ8)
Macromolecule: Serine/threonine-protein kinase Chk1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: MAVPFVEDWDLVQTLGEGSFGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.165
R free: 0.1998
Average B factor: 42.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% PEG 8000, 0.1 M MES buffer pH 6.5, 20% ethylene glycol
Matthews coefficient: 2.35
Solvent content (%): 47.74
Ligand: 5-(4-methylpiperazin-1-yl)-2-phenylmethoxy-~{N}-pyridin-3-yl-benzamide (A0Q)
Ligand formula: C24 H26 N4 O2
Ligand molecular weight: 402.489
Ligand SMILES: CN1CCN(CC1)c2ccc(c(c2)C(=O)Nc3cccnc3)OCc4ccccc4
Ligand InChI: InChI=1S/C24H26N4O2/c1-27-12-14-28(15-13-27)21-9-10-23(30-18-19-6-3-2-4-7-19)22(16-21)24(29)26-20-8-5-11-25-17-20/h2-11,16-17H,12-15,18H2,1H3,(H,26,29)
Release date: 2017-10-25
Crystal structure of human MTH1(G2K mutant) in complex with 2-oxo-dATP at pH 8.0 (PDB entry 8I1E)
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: MKASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.1
R work: 0.1424
R free: 0.1759
Average B factor: 19.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, tris, NaCl
Matthews coefficient: 1.89
Solvent content (%): 35.04
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2023-03-22
Human carbonic anhydrase IX mimic with Epacadostat bound (PDB entry 6VKG)
Macromolecule: human carbonic anhydrase IX mimic
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVDKALQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAEGVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.37
R work: 0.1269
R free: 0.1671
Average B factor: 14.28
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 200 nL 5.9 mg/mL protein + 200 nL reservoir (2.7 M ammonium sulfate, 50 mM Tris buffer, pH 8.2)
Matthews coefficient: 2.08
Solvent content (%): 40.9
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-03-04
Crystal structure of Aurora-A kinase in complex with an allosterically binding fragment (PDB entry 5ORS)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 265 residues
Sequence: QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.207
R free: 0.2573
Average B factor: 47.8867
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Tris, pH 8.5: 0.5 M NaCl: 0.2 M MgCl2: 32.5 % v/v PEG 3350
Matthews coefficient: 2.79
Solvent content (%): 55.9
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: 2017-11-01
Crystal structure of Akt1 in complex with a selective inhibitor (PDB entry 6CCY)
Macromolecule: RAC-alpha serine/threonine-protein kinase,PIFtide
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 343 residues
Sequence: GSLRVTMNEFEYLKLLGKGTFGKVILVKEKATGRYYAMKILKKEVIVAKDEVAHTLTESRVLQNSRHPFLTALKYSFQTHDRLCFVMEYANGGELFFHLSRERVFSEDRARFYGAEIVSALDYLHSEKNVVYRDLKLENLMLDKDGHIKITDFGLCKEGIKDGATMKTFCGTPEYLAPEVLEDNDYGRAVDWWGLGVVMYEMMCGRLPFYNQDHEKLFELILMEEIRFPRTLGPEAKSLLSGLLKKDPKQRLGGGPSDAKEIMQHRFFAGIVWQHVYEKKLSPPFKPQVTSEVDTRYFDEEFTAQMITITPPDQDDSMECVDSERREEQEMFRDFDYIADWEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.2352
R free: 0.276
Average B factor: 58.86
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 16% PEG 3350 and 200mM Ammonium Formate
Matthews coefficient: 2.28
Solvent content (%): 46.05
Ligand: (5R)-4-(4-{4-[4-fluoro-3-(trifluoromethyl)phenyl]-1-[2-(pyrrolidin-1-yl)ethyl]-1H-imidazol-2-yl}piperidin-1-yl)-5-methyl-5,8-dihydropyrido[2,3-d]pyrimidin-7(6H)-one (EX4)
Ligand formula: C29 H33 F4 N7 O
Ligand molecular weight: 571.612
Ligand SMILES: CC1CC(=O)Nc2c1c(ncn2)N3CCC(CC3)c4nc(cn4CCN5CCCC5)c6ccc(c(c6)C(F)(F)F)F
Ligand InChI: InChI=1S/C29H33F4N7O/c1-18-14-24(41)37-26-25(18)28(35-17-34-26)39-10-6-19(7-11-39)27-36-23(16-40(27)13-12-38-8-2-3-9-38)20-4-5-22(30)21(15-20)29(31,32)33/h4-5,15-19H,2-3,6-14H2,1H3,(H,34,35,37,41)/t18-/m1/s1
Release date: 2018-05-02
Human FKBP12 in complex with (1S,5S,6R)-10-((R)-(3,5-dichlorophenyl)sulfonimidoyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one (PDB entry 8CHJ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 107 residues
Sequence: GVQVETISPGDGRTFPKRGQTVVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.697
R work: 0.1828
R free: 0.2047
Average B factor: 25.864
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.32M Na-K tartrate, 0.2 M ammonium citrate, 0.1M MES pH 6.5
Matthews coefficient: 2.76
Solvent content (%): 55.4
Ligand: (1S,5S,6R)-10-[[3,5-bis(chloranyl)phenyl]sulfonimidoyl]-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one (UQI)
Ligand formula: C22 H24 Cl2 N4 O2 S
Ligand molecular weight: 479.423
Ligand SMILES: C=CC1CN(C(=O)C2CCCC1N2S(=N)(=O)c3cc(cc(c3)Cl)Cl)Cc4ccccn4
Ligand InChI: InChI=1S/C22H24Cl2N4O2S/c1-2-15-13-27(14-18-6-3-4-9-26-18)22(29)21-8-5-7-20(15)28(21)31(25,30)19-11-16(23)10-17(24)12-19/h2-4,6,9-12,15,20-21,25H,1,5,7-8,13-14H2/t15-,20+,21-,31+/m0/s1
Release date: 2023-09-06