satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human DNA polymerase eta incorporating ITP across dC (PDB entry 8G8H)
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): 1.64
R work: 0.2098
R free: 0.2415
Average B factor: 34.34
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: 2.14
Solvent content (%): 42.49
Ligand: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (CZU)
Ligand formula: C10 H15 N4 O14 P3
Ligand molecular weight: 508.166
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=CNC2=O
Ligand InChI: InChI=1S/C10H15N4O14P3/c15-6-4(1-25-30(21,22)28-31(23,24)27-29(18,19)20)26-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,21,22)(H,23,24)(H,11,12,17)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2024-02-21
Human Aurora A catalytic domain bound to FK1141 (PDB entry 4ZTR)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNCQNKESASKQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.21185
R free: 0.26781
Average B factor: 90.759
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M Tris pH 8.0, 
28% PEG 4k
Matthews coefficient: 2.6
Solvent content (%): 52.74
Ligand: 6-({4-[(Z)-{(2Z)-2-[(4-ethylphenyl)imino]-3-methyl-4-oxo-1,3-thiazolidin-5-ylidene}methyl]pyridin-2-yl}amino)pyridine-3-carboxylic acid (4RJ)
Ligand formula: C24 H21 N5 O3 S
Ligand molecular weight: 459.52
Ligand SMILES: CCc1ccc(cc1)N=C2N(C(=O)C(=Cc3ccnc(c3)Nc4ccc(cn4)C(=O)O)S2)C
Ligand InChI: InChI=1S/C24H21N5O3S/c1-3-15-4-7-18(8-5-15)27-24-29(2)22(30)19(33-24)12-16-10-11-25-21(13-16)28-20-9-6-17(14-26-20)23(31)32/h4-14H,3H2,1-2H3,(H,31,32)(H,25,26,28)/b19-12-,27-24-
Release date: 2016-07-20
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL,beta-gamma dTTP analogue (PDB entry 6CTN)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACAGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.92
R work: 0.1866
R free: 0.2347
Average B factor: 28.0978
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.3
Solvent content (%): 46.41
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-06-20
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOMB000141a (PDB entry 5QES)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.745
R work: 0.1832
R free: 0.2044
Average B factor: 39.6353
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: well solution: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.33
Solvent content (%): 63.12
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2018-10-10
Crystal structure of the PTPN3 PDZ domain bound to the PBM TACE C-terminal peptide (PDB entry 8CQY)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 114 residues
Sequence: GAMGSSTEDASQYYCDKNDNGDSYLVLIRITPDEDGKFGFNLKGGVDQKMPLVVSRINPESPADTCIPKLNEGDQIVLINGRDISEHTHDQVVMFIKASRESHSRELALVIRRR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.16756
R free: 0.20258
Average B factor: 42.01
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 20% w/v PEG 3350, 0.2 M NaSCN at pH 7
Matthews coefficient: 2.78
Solvent content (%): 55.81
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2023-05-10
Crystal Structure of the Human CAMKK1A in complex with Hesperadin (PDB entry 6CCF)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 290 residues
Sequence: SMQLNQYKLQSEIGKGAYGVVRLAYNESEDRHYAMKVLSKKKLLKQYGFPRRPPPRGSQAAQGGPAKQLLPLERVYQEIAILKKLDHVNVVKLIEVLDDPAEDNLYLVFDLLRKGPVMEVPCDKPFSEEQARLYLRDVILGLEYLHCQKIVHRDIKPSNLLLGDDGHVKIADFGVSNQFEGNDAQLSSTAGTPAFMAPEAISDSGQSFSGKALDVWATGVTLYCFVYGKCPFIDDFILALHRKIKNEPVVFPEEPEISEELKDLILKMLDKNPETRIGVPDIKLHPWVTK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.21049
R free: 0.24384
Average B factor: 34.479
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 280
Crystal growth procedure: 33% PEG2000 MME, 0.1 M potassium thiocyanate, 0.1 M CHC buffer, pH 7.5, cryoprotectant: 30% polyethylene glycol
Matthews coefficient: 2.49
Solvent content (%): 50.55
Ligand: N-[2-OXO-3-((E)-PHENYL{[4-(PIPERIDIN-1-YLMETHYL)PHENYL]IMINO}METHYL)-2,6-DIHYDRO-1H-INDOL-5-YL]ETHANESULFONAMIDE (H1N)
Ligand formula: C29 H32 N4 O3 S
Ligand molecular weight: 516.654
Ligand SMILES: CCS(=O)(=O)Nc1ccc2c(c1)C(C(=O)N2)C(=Nc3ccc(cc3)CN4CCCCC4)c5ccccc5
Ligand InChI: InChI=1S/C29H32N4O3S/c1-2-37(35,36)32-24-15-16-26-25(19-24)27(29(34)31-26)28(22-9-5-3-6-10-22)30-23-13-11-21(12-14-23)20-33-17-7-4-8-18-33/h3,5-6,9-16,19,27,32H,2,4,7-8,17-18,20H2,1H3,(H,31,34)/b30-28+/t27-/m0/s1
Release date: 2018-03-07
Thrombin in Complex with a D-DiPhe-Pro-p-pyridine derivative (PDB entry 6TDT)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 259 residues
Sequence: IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1596
R free: 0.1769
Average B factor: 21.16
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM Sodium dihydrogen phosphate, 350 mM NaCl, 27% (w/v) PEG 8000
Matthews coefficient: 2.51
Solvent content (%): 51.07
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: 2020-05-13
The Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)-2-(5-chlorothiophen-2-yl)propanoyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid (PDB entry 8CCC)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 128 residues
Sequence: GAPATVTEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEIAHLLIKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.2161
R free: 0.2389
Average B factor: 32.336
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate
Matthews coefficient: 2.57
Solvent content (%): 52.1
Ligand: 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-(5-chloranylthiophen-2-yl)propanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid (UCT)
Ligand formula: C32 H36 Cl N O8 S
Ligand molecular weight: 630.148
Ligand SMILES: CC(c1ccc(s1)Cl)C(=O)N2CCCCC2C(=O)OC(CCc3ccc(c(c3)OC)OC)c4cccc(c4)OCC(=O)O
Ligand InChI: InChI=1S/C32H36ClNO8S/c1-20(28-14-15-29(33)43-28)31(37)34-16-5-4-9-24(34)32(38)42-25(22-7-6-8-23(18-22)41-19-30(35)36)12-10-21-11-13-26(39-2)27(17-21)40-3/h6-8,11,13-15,17-18,20,24-25H,4-5,9-10,12,16,19H2,1-3H3,(H,35,36)/t20-,24+,25-/m1/s1
Release date: 2023-04-26
Human VKOR C43S mutant with vitamin K1 epoxide (PDB entry 6WV5)
Macromolecule: Vitamin K epoxide reductase Cys43Ser mutant, 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: MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNSTWGSPGWVRLALCLTGLVLSLYALHVKAARARDRDYRALSDVGTAISCSRVFSSRWGRGFGLVEHVLGQDSILNQSNSIFGCIFYTLQLLLGCLRTRWASVLMLLSSLVSLAGSVYLAWILFFVLYDFCIVCITTYAINVSLMWLSFRKVQENSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHHHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2311
R free: 0.2704
Average B factor: 62.1792
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6.5
Crystallization temperature (K): 295
Crystal growth procedure: 25% PEG400, 0.1 M ammonium citrate dibasic, 0.1 M MES, pH 6.5
Matthews coefficient: 3.96
Solvent content (%): 68.94
Ligand: (2R,3R)-2-hydroxy-3-methyl-2-[(2E,7S)-3,7,11,15-tetramethylhexadec-2-en-1-yl]-2,3-dihydronaphthalene-1,4-dione (UAV)
Ligand formula: C31 H48 O3
Ligand molecular weight: 468.711
Ligand SMILES: CC1C(=O)c2ccccc2C(=O)C1(CC=C(C)CCCC(C)CCCC(C)CCCC(C)C)O
Ligand InChI: InChI=1S/C31H48O3/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-31(34)26(6)29(32)27-18-7-8-19-28(27)30(31)33/h7-8,18-20,22-24,26,34H,9-17,21H2,1-6H3/b25-20+/t23?,24-,26-,31+/m0/s1
Release date: 2020-11-11
Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2-001 (PDB entry 7ZMM)
Macromolecule: ATP-dependent DNA helicase Q5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 445 residues
Sequence: SMDPERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGAGKSLCYQLPALLAKGITIVVSPLIALIQDQVDHLLTLKVRVSSLNSKLSAQERKELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFRPDYLRLGALRSRLGHAPCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDVQFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAYHAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEKRGNKASDKATIMAFDALVTFCEELGCRHAAIAKYFGDALPACAKGCDHCQNPTAVRRRLEALERSSSW
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2356
R free: 0.2806
Average B factor: 79.866
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5
Matthews coefficient: 2.68
Solvent content (%): 54.13
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: 2022-06-22
Designed Enzyme SH3-588 (Catechol O-methyltransferase catalytic domain and Src homology 3 binding domain fusion) (PDB entry 7UD6)
Macromolecule: Tyrosine-protein kinase Fyn,Catechol O-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.6
Sequence length: 293 residues
Sequence: MLFVALYDYEARTEDDLSFHKGEKFVILRSSEGDWWLAVSLTTGEQGYIPSNYVAPVGGSGGSGGTKEQRILEFVQLVAKPGDPQSVLEAIDQYCTYAEWAMNVGDAKGQIMDAVIREYSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEINPDCAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKYDVDTLDMVFLDHWKDRYLPDTLLLEKCGLLRKGTVLLADNVIVPGTPDFLAYVRGSSSFECTHYSSYLEYMKVVDGLEKAIYQGPGENLYFQSAGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.59
R work: 0.2466
R free: 0.2779
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 297
Crystal growth procedure: 0.7 M magnesium formate, 0.1 M bis-tris propone pH 7.0.
Matthews coefficient: 3.41
Solvent content (%): 63.93
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2023-01-11
Native state mass spectrometry, surface plasmon resonance and X-ray crystallography correlate strongly as a fragment screening combination (PDB entry 5FLR)
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): 1.68
R work: 0.14663
R free: 0.2046
Average B factor: 16.523
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystal growth procedure: 15 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C IN SITTING DROPS.
Matthews coefficient: 2.1
Solvent content (%): 42.1
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2016-03-02
FGFR1 kinase domain with a covalent inhibitor 9g (PDB entry 8Y22)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 308 residues
Sequence: AGVSEYELPEDPRWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.792
R work: 0.1937
R free: 0.2597
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG 8000, 0.2 M Li2SO4, and 0.1 M MES, pH 6.5
Matthews coefficient: 2.64
Solvent content (%): 53.46
Ligand: ~{N}-[4-[[4-azanyl-3-(7-methoxy-5-methyl-1-benzothiophen-2-yl)pyrazolo[3,4-d]pyrimidin-1-yl]methyl]phenyl]propanamide (A1LW9)
Ligand formula: C25 H24 N6 O2 S
Ligand molecular weight: 472.562
Ligand SMILES: CCC(=O)Nc1ccc(cc1)Cn2c3c(c(n2)c4cc5cc(cc(c5s4)OC)C)c(ncn3)N
Ligand InChI: InChI=1S/C25H24N6O2S/c1-4-20(32)29-17-7-5-15(6-8-17)12-31-25-21(24(26)27-13-28-25)22(30-31)19-11-16-9-14(2)10-18(33-3)23(16)34-19/h5-11,13H,4,12H2,1-3H3,(H,29,32)(H2,26,27,28)
Release date: 2024-06-26
Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosyl 1,3,4-trisphosphate/AMP-PNP/Mg (PDB entry 8PPF)
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): 1.85
R work: 0.19563
R free: 0.22779
Average B factor: 42.004
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.81 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, 5 mM ligand, 3 mM AMP-PNP and 3 mM MgCl2.
Matthews coefficient: 2.71
Solvent content (%): 54.72
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2024-02-28
Notum_Maybridge_56 (PDB entry 7BLU)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.21
R work: 0.193
R free: 0.1888
Average B factor: 17.4254
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.95
Solvent content (%): 36.8
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: 2022-03-02
Crystal structure of protein tyrosine phosphatase Shp2 catalytic domain complex with small molecular compound L88N79 (PDB entry 4PVG)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 298 residues
Sequence: MTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2361
R free: 0.2865
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.7
Crystallization temperature (K): 298
Crystal growth procedure: 30% w/v polyethylene glycol 3350, 100 mM NaCl, 1mM L88N79 and 100mM HEPES (pH 7.7) , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Matthews coefficient: 1.99
Solvent content (%): 38.08
Ligand: 2-[3-({4-[(1,3-benzodioxol-5-ylmethyl)amino]-4-oxobutanoyl}amino)phenyl]-6-hydroxy-3-iodo-1-methyl-1H-indole-5-carboxylic acid (2WT)
Ligand formula: C28 H24 I N3 O7
Ligand molecular weight: 641.411
Ligand SMILES: Cn1c2cc(c(cc2c(c1c3cccc(c3)NC(=O)CCC(=O)NCc4ccc5c(c4)OCO5)I)C(=O)O)O
Ligand InChI: InChI=1S/C28H24IN3O7/c1-32-20-12-21(33)19(28(36)37)11-18(20)26(29)27(32)16-3-2-4-17(10-16)31-25(35)8-7-24(34)30-13-15-5-6-22-23(9-15)39-14-38-22/h2-6,9-12,33H,7-8,13-14H2,1H3,(H,30,34)(H,31,35)(H,36,37)
Release date: 2015-04-15
Discovery of MK-8189, a highly potent and selective PDE10A inhibitor for the treatment of schizophrenia (PDB entry 8DI4)
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: 345 residues
Sequence: GSHMSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGEETATWISSPSVAQKAAASED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.016
R work: 0.2499
R free: 0.2946
Average B factor: 48.45
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG3350, 0.2M MgCl2, 10mM 2-Mercaptoethanol, 0.1M HEPES, pH7.0
Matthews coefficient: 2.01
Solvent content (%): 38.94
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2023-02-08
CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE PDZ BINDING MOTIF OF THE MITOGEN ACTIVATED PROTEIN KINASE P38GAMMA. (PDB entry 5EZ0)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 107 residues
Sequence: GSSPEKPTPNGGIPHDNLVLIRMKPDENGRFGFNVKGGYDQKMPVIVSRVAPGTPADLCVPRLNEGDQVVLINGRDIAEHTHDQVVLFIKASCERHSGELMLLVRPN
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.2284
R free: 0.2517
Average B factor: 45.07
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 10.5
Crystallization temperature (K): 291
Crystal growth procedure: 1.2 M SODIUM DI-HYDROGEN PHOSPHATE 0.8 M DI-POTASSIUM HYDROGEN PHOSPHATE 0.1M CAPS
0.2 M Lithium sulfate
0.67 M Non-Detergent Sulfobetaine (NDSB) 201
Matthews coefficient: 2.45
Solvent content (%): 49.83
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: 2016-06-08