satarupa22/MacromolecularLigandDB huggingface dataset:
Human GAR transformylase in complex with GAR substrate and AGF291 inhibitor (PDB entry 8FJY)
Macromolecule: Trifunctional purine biosynthetic protein adenosine-3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.4.13
Sequence length: 210 residues
Sequence: MARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWVKEEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.98
R work: 0.2059
R free: 0.2511
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Tris (pH 7.5), 0.333 mM NaCl, 20% polyethylene glycol (PEG) 4000, and 2% PEG 400
Matthews coefficient: 3.63
Solvent content (%): 66.14
Ligand: GLYCINAMIDE RIBONUCLEOTIDE (GAR)
Ligand formula: C7 H13 N2 O8 P
Ligand molecular weight: 284.16
Ligand SMILES: C(C1C(C(C(O1)NC(=O)CN)O)O)OP(=O)([O-])[O-]
Ligand InChI: InChI=1S/C7H15N2O8P/c8-1-4(10)9-7-6(12)5(11)3(17-7)2-16-18(13,14)15/h3,5-7,11-12H,1-2,8H2,(H,9,10)(H2,13,14,15)/p-2/t3-,5-,6-,7-/m1/s1
Release date: 2023-09-06
A fragment-based inhibitor of SHP2 (PDB entry 8S0J)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 537 residues
Sequence: HMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.89
R work: 0.20004
R free: 0.24227
Average B factor: 46.417
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 0.5M K formate
15% PEG 3350
0.1M pH=8 Bis-Tris propane/HCl
Matthews coefficient: 2.21
Solvent content (%): 44.22
Ligand: 3-[3-[2,3-bis(chloranyl)phenyl]-1H-pyrrolo[3,2-b]pyridin-6-yl]propan-1-amine (A1H4R)
Ligand formula: C16 H15 Cl2 N3
Ligand molecular weight: 320.216
Ligand SMILES: c1cc(c(c(c1)Cl)Cl)c2c[nH]c3c2ncc(c3)CCCN
Ligand InChI: InChI=1S/C16H15Cl2N3/c17-13-5-1-4-11(15(13)18)12-9-20-14-7-10(3-2-6-19)8-21-16(12)14/h1,4-5,7-9,20H,2-3,6,19H2
Release date: 2024-03-20
The structure of p38 alpha in complex with a triazol inhibitor (PDB entry 5XYY)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 380 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1786
R free: 0.2007
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 298
Crystal growth procedure: Sodium citrate, Ammonium sulfate, HEPES
Matthews coefficient: 3.02
Solvent content (%): 59.29
Ligand: 3-(5-{[(2-chloro-6-fluorophenyl)methyl]amino}-4H-1,2,4-triazol-3-yl)phenol (P0F)
Ligand formula: C15 H12 Cl F N4 O
Ligand molecular weight: 318.733
Ligand SMILES: c1cc(cc(c1)O)c2[nH]c(nn2)NCc3c(cccc3Cl)F
Ligand InChI: InChI=1S/C15H12ClFN4O/c16-12-5-2-6-13(17)11(12)8-18-15-19-14(20-21-15)9-3-1-4-10(22)7-9/h1-7,22H,8H2,(H2,18,19,20,21)
Release date: 2018-01-17
Structure of Compound 5 bound to the CHK1 10-point mutant (PDB entry 8SIW)
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: MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTEEAVAVKIVDMKRAVDCPENIKKEICILKMLNHENVIKFYGHRREGNIQYLFMELASGGSLFDRIEPDIGMPEPDAQRFFHQLMAGVVYLHGIGITHRDIKPHNLLLDERDNLKIADYSLATVFRYNNRERLLNKMCGTLPYVAPELLKRREFHAEPVDVWSCGIVLTAMLAGELPWDQPSDSCQEYSDWKEKKTYLNPWKKIDSAPLALLHKILVENPSARITIPDIKKDRWYNKPLKKGAKRPRVTSGGVSESPSGHHHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.877
R work: 0.2188
R free: 0.2581
Average B factor: 39.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 11% PEG 8000, 15-20% ethylene glycol, 0.1 M MES (pH 6.5), 5% 6-aminohexanoic acid
Matthews coefficient: 2.36
Solvent content (%): 47.88
Ligand: (1S,2S)-N-(7-chloro-6-{1-[(3R,4R)-4-hydroxy-3-methyloxolan-3-yl]piperidin-4-yl}isoquinolin-3-yl)-2-(1-methyl-1H-pyrazol-4-yl)cyclopropane-1-carboxamide (ZXL)
Ligand formula: C27 H32 Cl N5 O3
Ligand molecular weight: 510.028
Ligand SMILES: CC1(COCC1O)N2CCC(CC2)c3cc4cc(ncc4cc3Cl)NC(=O)C5CC5c6cnn(c6)C
Ligand InChI: InChI=1S/C27H32ClN5O3/c1-27(15-36-14-24(27)34)33-5-3-16(4-6-33)21-7-17-9-25(29-11-18(17)8-23(21)28)31-26(35)22-10-20(22)19-12-30-32(2)13-19/h7-9,11-13,16,20,22,24,34H,3-6,10,14-15H2,1-2H3,(H,29,31,35)/t20-,22+,24+,27-/m1/s1
Release date: 2023-11-01
Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present. (PDB entry 6WI2)
Macromolecule: Cysteine desulfurase, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.8.1.7
Sequence length: 406 residues
Sequence: MGSSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASLIGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQVTYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDAAQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRSGTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFTTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1504
R free: 0.1849
Average B factor: 41.8796
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 288
Crystal growth procedure: 0.1 M MES pH 5.5
22.5 % PEG 400
Matthews coefficient: 2.88
Solvent content (%): 57.23
Ligand: PYRIDOXAL-5'-PHOSPHATE (PLP)
Ligand formula: C8 H10 N O6 P
Ligand molecular weight: 247.142
Ligand SMILES: Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
Ligand InChI: InChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
Release date: 2020-04-22
Crystal structure of human MTH1(G2K mutant) in complex with 8-oxo-dGTP (PDB entry 5GHI)
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): 1.211
R work: 0.1359
R free: 0.1718
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: sodium citrate, sodium cacodylate, NaCl
Matthews coefficient: 1.89
Solvent content (%): 35.09
Ligand: 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (8DG)
Ligand formula: C10 H16 N5 O14 P3
Ligand molecular weight: 523.18
Ligand SMILES: C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C10H16N5O14P3/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(27-5)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
Release date: 2017-01-04
Crystal structure of BACE complex with BMC014 (PDB entry 5QD7)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 402 residues
Sequence: GPDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.165
R free: 0.188
Average B factor: 53.04
Crystallization method: hanging drop
Crystallization temperature (K): 292
Crystal growth procedure: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS FROM 1.0M AMMONIUM SULFATE IN WATER. PROTEIN STOCK WAS
BACE MUT46B BATCH XVI 7.0MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 6-FOLD EXCESS OF BMC014 ADDED FROM A 50MM
STOCK SOLUTION IN 90% DMSO-D6 (1.7% DMSO IN DROP). A SOLUTION CONTAINING 1.2M AMMONIUM SULFATE, 25% (V/V) GLYCEROL,
1.0MM BMC014 WAS USED AS CRYO-PROTECTANT.
Matthews coefficient: 3.05
Solvent content (%): 59.61
Ligand: (4S)-4-[(1R)-1-hydroxy-2-({1-[3-(1-methylethyl)phenyl]cyclopropyl}amino)ethyl]-19-(methoxymethyl)-11-oxa-3,16-diazatric
yclo[15.3.1.1~6,10~]docosa-1(21),6(22),7,9,17,19-hexaen-2-one (0BI)
Ligand formula: C35 H45 N3 O4
Ligand molecular weight: 571.749
Ligand SMILES: CC(C)c1cccc(c1)C2(CC2)NCC(C3Cc4cccc(c4)OCCCCNc5cc(cc(c5)C(=O)N3)COC)O
Ligand InChI: InChI=1S/C35H45N3O4/c1-24(2)27-9-7-10-29(20-27)35(12-13-35)37-22-33(39)32-19-25-8-6-11-31(18-25)42-15-5-4-14-36-30-17-26(23-41-3)16-28(21-30)34(40)38-32/h6-11,16-18,20-21,24,32-33,36-37,39H,4-5,12-15,19,22-23H2,1-3H3,(H,38,40)/t32-,33+/m0/s1
Release date: 2020-06-03
VDR complex with BXL-62 (PDB entry 7BNS)
Macromolecule: Vitamin D3 receptor A
Type: Protein, polypeptide(L)
Source organism: Danio rerio
Sequence length: 302 residues
Sequence: GSHMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNHSPESVDTKLNFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEVS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.1768
R free: 0.2599
Average B factor: 71.2052
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 273
Crystal growth procedure: 50 mM Bis-Tris pH 6.5, 1.6 M lithium sulfate and 50 mM magnesium sulfate
Matthews coefficient: 2.3
Solvent content (%): 46.62
Ligand: 1,25-Dihydroxy-16-ene-20-cyclopropyl-vitamin D3 (U5W)
Ligand formula: C28 H42 O3
Ligand molecular weight: 426.631
Ligand SMILES: CC12CCCC(=CC=C3CC(CC(C3=C)O)O)C1CC=C2C4(CC4)CCCC(C)(C)O
Ligand InChI: InChI=1S/C28H42O3/c1-19-21(17-22(29)18-24(19)30)9-8-20-7-5-13-27(4)23(20)10-11-25(27)28(15-16-28)14-6-12-26(2,3)31/h8-9,11,22-24,29-31H,1,5-7,10,12-18H2,2-4H3/b20-8+,21-9-/t22-,23+,24+,27+/m1/s1
Release date: 2022-03-02
Crystal structure of CBP bromodomain liganded with CCS150 (PDB entry 7XI0)
Macromolecule: CREB-binding protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 133 residues
Sequence: MKKGHHHHHHLVPRGSRKKIFKPEELRQALMPTLEALYRQDPESLPFRQPVDPQLLGIPDYFDIVKNPMDLSTIKRKLDTGQYQEPWQYVDDVWLMFNNAWLYNRKTSRVYKFCSKLAEVFEQEIDPVMQSLG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62
R work: 0.1919
R free: 0.2244
Average B factor: 21.745
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2M NaAc, 20% w/v Polyethylene glycol, 3350   PH 7.3
Matthews coefficient: 2.03
Solvent content (%): 39.32
Ligand: (6S)-1-(3-chloranyl-4-methoxy-phenyl)-6-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(3R)-1-methylsulfonylpyrrolidin-3-yl]benzimidazol-2-yl]piperidin-2-one (EL0)
Ligand formula: C29 H32 Cl N5 O5 S
Ligand molecular weight: 598.113
Ligand SMILES: Cc1c(c(on1)C)c2ccc3c(c2)nc(n3C4CCN(C4)S(=O)(=O)C)C5CCCC(=O)N5c6ccc(c(c6)Cl)OC
Ligand InChI: InChI=1S/C29H32ClN5O5S/c1-17-28(18(2)40-32-17)19-8-10-24-23(14-19)31-29(35(24)21-12-13-33(16-21)41(4,37)38)25-6-5-7-27(36)34(25)20-9-11-26(39-3)22(30)15-20/h8-11,14-15,21,25H,5-7,12-13,16H2,1-4H3/t21-,25+/m1/s1
Release date: 2022-07-27
The structure of Stable-5-Lipoxygenase bound to NDGA (PDB entry 6N2W)
Macromolecule: Arachidonate 5-lipoxygenase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.34
Sequence length: 691 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMPSYTVTVATGSQEHAGTDDYIYLSLVGSAGCSEKHLLDKGSFERGAVDSYDVTVDEELGEIQLVRIEKRKYGSNDDWYLKYITLKTPHGDYIEFPCYRWITGDVEVVLRDGRAKLARDDQIHILKQHRRKELETRQKQYRWMEWNPGFPLSIDAKCHKDLPRDIQFDSEKGVDFVLNYSKAMENLFINRFMHMFQSSWNDFADFEKIFVKISNTISERVMNHWQEDLMFGYQFLNGANPVLIRRCTELPEKLPVTTEMVECSLERQLSLEQEVQQGNIFIVDFELLDGIDANKTDPCTLQFLAAPICLLYKNLANKIVPIAIQLNQIPGDENPIFLPSDAKYDWLLAKIWVRSSDFHVHQTITHLLRTHLVSEVFGIAMYRQLPAVHPIFKLLVAHVRFTIAINTKAREQLICECGLFDKANATGGGGHVQMVQRAMKDLTYASLCFPEAIKARGMESKEDIPYYFYRDDGLLVWEAIRTFTAEVVDIYYEGDQVVEEDPELQDFVNDVYVYGMRGRKSSGFPKSVKSREQLSEYLTVVIFTASAQHAAVNFGQYDWASWIPNAPPTMRAPPPTAKGVVTIEQIVDTLPDRGRSCWHLGAVWALSQFQENELFLGMYPEEHFIEKPVKEAMARFRKNLEAIVSVIAERNENLQLPYYYLSPDRIPNSVAI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.71
R work: 0.2129
R free: 0.2626
Average B factor: 49.54
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 8-10% Tacsimate
Matthews coefficient: 2.34
Solvent content (%): 47.44
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2020-05-13
IRAK4 in complex with Compound 21 (PDB entry 5K72)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 301 residues
Sequence: VSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.22
R work: 0.215
R free: 0.225
Average B factor: 63.49
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2.5 M ammonium sulfate, 0.1 M Hepes pH 7.2
Matthews coefficient: 2.69
Solvent content (%): 54.31
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2017-12-06
Crystal structure of the WDR domain of human DCAF1 in complex with OICR-6766 (PDB entry 7UFV)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 315 residues
Sequence: GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.204
R free: 0.254
Average B factor: 42.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 0.2M Potassium Fluoride
Matthews coefficient: 2.21
Solvent content (%): 44.44
Ligand: (3P)-N-[(1S)-3-amino-1-(3-chlorophenyl)-3-oxopropyl]-3-(2-fluorophenyl)-1H-pyrazole-4-carboxamide (N6O)
Ligand formula: C19 H16 Cl F N4 O2
Ligand molecular weight: 386.807
Ligand SMILES: c1ccc(c(c1)c2c(c[nH]n2)C(=O)NC(CC(=O)N)c3cccc(c3)Cl)F
Ligand InChI: InChI=1S/C19H16ClFN4O2/c20-12-5-3-4-11(8-12)16(9-17(22)26)24-19(27)14-10-23-25-18(14)13-6-1-2-7-15(13)21/h1-8,10,16H,9H2,(H2,22,26)(H,23,25)(H,24,27)/t16-/m0/s1
Release date: 2022-05-04
PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine (PDB entry 4ZJI)
Macromolecule: Serine/threonine-protein kinase PAK 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 299 residues
Sequence: GPSDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRDIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.99
R work: 0.1909
R free: 0.2198
Average B factor: 33.21
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: Equal volumes (1.0 uL) of reservoir solution and protein solution were mixed. Reservoir solution: 17.2% (w/v) PEG3350, 0.2 M magnesium formate (dihydrate)
Matthews coefficient: 2.77
Solvent content (%): 55.56
Ligand: 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine (4OQ)
Ligand formula: C20 H22 Cl F N4
Ligand molecular weight: 372.867
Ligand SMILES: CCN1c2ccc(cc2C(=Nc3c1ccc(c3)F)N4CCN(CC4)C)Cl
Ligand InChI: InChI=1S/C20H22ClFN4/c1-3-26-18-6-4-14(21)12-16(18)20(25-10-8-24(2)9-11-25)23-17-13-15(22)5-7-19(17)26/h4-7,12-13H,3,8-11H2,1-2H3
Release date: 2015-06-24
Crystal structure of BACE1 with a pyrazole-substituted tetrahydropyran thioamidine (PDB entry 4XXS)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 415 residues
Sequence: ETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDESTHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1818
R free: 0.2076
Average B factor: 50.02
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 291
Crystal growth procedure: BACE1 lacking the pro-segment was concentrated to ~14 mg/mL in 20 mM Tris pH 7.4 and 250 mM NaCl.  Crystallization was carried out by the vapor diffusion method against 200 mM sodium citrate tribasic dihydrate, 22% PEG 5K monomethyl ether and 200 mM ammonium iodide.
Matthews coefficient: 2.78
Solvent content (%): 55.7
Ligand: (4aR,6R,8aS)-8a-(2,4-difluorophenyl)-6-(1-methyl-1H-pyrazol-4-yl)-4,4a,5,6,8,8a-hexahydropyrano[3,4-d][1,3]thiazin-2-amine (SI5)
Ligand formula: C17 H18 F2 N4 O S
Ligand molecular weight: 364.413
Ligand SMILES: Cn1cc(cn1)C2CC3CSC(=NC3(CO2)c4ccc(cc4F)F)N
Ligand InChI: InChI=1S/C17H18F2N4OS/c1-23-7-10(6-21-23)15-4-11-8-25-16(20)22-17(11,9-24-15)13-3-2-12(18)5-14(13)19/h2-3,5-7,11,15H,4,8-9H2,1H3,(H2,20,22)/t11-,15+,17-/m0/s1
Release date: 2015-04-01
The crystal structure of Lp-PLA2 in complex with a novel inhibitor (PDB entry 5YE8)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: GPLGSAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.851
R work: 0.1806
R free: 0.2119
Average B factor: 20.2874
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MOPS pH 6.6, 0.4M Li2SO4, 27% (w/v) (NH4)2SO4, 1M Na-Ac, 1.4% 1,4-butanediol
Matthews coefficient: 2.39
Solvent content (%): 48.47
Ligand: N-[3,4-bis(fluoranyl)phenyl]methanesulfonamide (8U3)
Ligand formula: C7 H7 F2 N O2 S
Ligand molecular weight: 207.198
Ligand SMILES: CS(=O)(=O)Nc1ccc(c(c1)F)F
Ligand InChI: InChI=1S/C7H7F2NO2S/c1-13(11,12)10-5-2-3-6(8)7(9)4-5/h2-4,10H,1H3
Release date: 2018-07-25
Crystal Structure of Human Pirin in complex with a Chemical Probe pyrrolidine 24 (PDB entry 5JCT)
Macromolecule: Pirin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.24
Sequence length: 310 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMGSSKKVTLSVLSREQSEGVGARVRRSIGRPELKNLDPFLLFDEFKGGRPGGFPDHPHRGFETVSYLLEGGSMAHEDFCGHTGKMNPGDLQWMTAGRGILHAEMPCSEEPAHGLQLWVNLRSSEKMVEPQYQELKSEEIPKPSKDGVTVAVISGEALGIKSKVYTRTPTLYLDFKLDPGAKHSQPIPKGWTSFIYTISGDVYIGPDDAQQKIEPHHTAVLGEGDSVQVENKDPKRSHFVLIAGEPLREPVIQHGPFVMNTNEEISQAILDFRNAKNGFERAKTWKSKIGN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.73
R work: 0.171
R free: 0.204
Average B factor: 32.2
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M HEPES (pH7.5), 8% (v/v) Eythylene Glycol, 20% (w/v) PEG 8000
Matthews coefficient: 2.22
Solvent content (%): 44.48
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2017-01-11
Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules (PDB entry 7US1)
Macromolecule: E3 ubiquitin-protein ligase parkin
Type: Protein, polypeptide(L)
Source organism: Rattus norvegicus
EC number: 2.3.2.31
Sequence length: 240 residues
Sequence: GPLGSSFFVYCKGPCHKVQPGKLRVQCGTCRQATLTLAQGPSCWDDVLIPNRMSGECQSPDCPGTRAEFFFKCGAHPTSDKDTSVALNLITNNSRSIPCIACTDVRNPVLVFQCNHRHVICLDCFHLYCVTRLNDRQFVHDAQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEQGQRKVTCEGGNGLGCGFVFCRDCKEAYHEGECDS
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.484
R work: 0.2294
R free: 0.2584
Average B factor: 77.6442
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1M Bis-Tris propane pH 7.5, 20.5% PEG3350, 0.2M NaI
Matthews coefficient: 2.93
Solvent content (%): 57.95
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