satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the indoleamine 2,3-dioxygenagse 1 (IDO1) complexed with NLG919 analogue (PDB entry 5EK2)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 403 residues
Sequence: MAHAMENSWTISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.68
R work: 0.1708
R free: 0.2314
Average B factor: 69.0602
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: PEG, Ammonium Fluoride
Matthews coefficient: 3.01
Solvent content (%): 59.19
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2015-12-23
Crystal structure of MMP12 in complex with carboxylic inhibitor LP165. (PDB entry 6EOX)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.142
R free: 0.179
Average B factor: 18.43
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: Drop: 1 micro-L (hMMP-12 at 855 micro-M + 1 milli-M hydroxamic acid + 1 milli-M LP165) and 1 micro-L reservoir solution.
Precipitant: 17% PEG 20K, 0.2M imidazole malate
250mM NaCl, pH 8.5.
Cryoprotection: 40% MPEG 5K, 10% 1,2-propanediol, 10% AAB (sodium acetate, ADA, bicine: 90% basic/10% acid), pH 8.0
Matthews coefficient: 2.11
Solvent content (%): 41.76
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: 2018-05-16
Crystal structure of phosphorylated RET tyrosine kinase domain complexed with a pyrazolo[1,5-a]pyrimidine inhibitor (PDB entry 6VHG)
Macromolecule: Proto-oncogene tyrosine-protein kinase receptor Ret
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GASVDAFKILEDPKWEFPRKNLVLGKTLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYGSLRGFLRESRKVGPGYLGSGGSRNSSSLDHPDERALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDSYVKRSQGRIPVKWMAIESLFDHIYTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVKRR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.303
R work: 0.2028
R free: 0.2377
Average B factor: 35.13
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293.15
Crystal growth procedure: 1.8M ammonium sulfate, 0.1M sodium acetate pH 4.6
Matthews coefficient: 2.8
Solvent content (%): 56.04
Ligand: 3-(3,4-dimethoxyphenyl)-N~5~-(1-methylpiperidin-4-yl)-6-phenylpyrazolo[1,5-a]pyrimidine-5,7-diamine (QX1)
Ligand formula: C26 H30 N6 O2
Ligand molecular weight: 458.555
Ligand SMILES: CN1CCC(CC1)Nc2c(c(n3c(n2)c(cn3)c4ccc(c(c4)OC)OC)N)c5ccccc5
Ligand InChI: InChI=1S/C26H30N6O2/c1-31-13-11-19(12-14-31)29-25-23(17-7-5-4-6-8-17)24(27)32-26(30-25)20(16-28-32)18-9-10-21(33-2)22(15-18)34-3/h4-10,15-16,19H,11-14,27H2,1-3H3,(H,29,30)
Release date: 2020-02-26
Discovery of IRAK4 Inhibitor 23 (PDB entry 8ATL)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 298 residues
Sequence: GSFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIAAAIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.464
R work: 0.1988
R free: 0.2429
Average B factor: 56.279
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.9
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M sodium acetate buffer pH 4.9, 2.13-2.145M sodium malonate
Matthews coefficient: 2.82
Solvent content (%): 56.4
Ligand: ~{N}-[6-methoxy-2-(2-morpholin-4-yl-2-oxidanylidene-ethyl)indazol-5-yl]-6-[(1~{R})-2,2,2-tris(fluoranyl)-1-oxidanyl-ethyl]pyridine-2-carboxamide (O6X)
Ligand formula: C22 H22 F3 N5 O5
Ligand molecular weight: 493.436
Ligand SMILES: COc1cc2c(cc1NC(=O)c3cccc(n3)C(C(F)(F)F)O)cn(n2)CC(=O)N4CCOCC4
Ligand InChI: InChI=1S/C22H22F3N5O5/c1-34-18-10-16-13(11-30(28-16)12-19(31)29-5-7-35-8-6-29)9-17(18)27-21(33)15-4-2-3-14(26-15)20(32)22(23,24)25/h2-4,9-11,20,32H,5-8,12H2,1H3,(H,27,33)/t20-/m1/s1
Release date: 2023-09-06
Aurora-A in complex with shape-diverse fragment 55 (PDB entry 6R4A)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 285 residues
Sequence: GAMESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNAQNKESASKQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.937
R work: 0.1905
R free: 0.2339
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: 2.55
Solvent content (%): 51.78
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: 2019-05-08
Structure of PP1-Phactr1 chimera [PP1(7-304) + linker (SGSGS) + Phactr1(526-580)] (PDB entry 6ZEJ)
Macromolecule: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Phosphatase and actin regulator
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 363 residues
Sequence: GHMGSLNLDSIIGRLLEVQGSRPGKNVQLTENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDECKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDVQGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVDETLMCSFQILKPADKNKGSGSGSVEVADAQDYDRRADKPWTRLTAADKAAIRKELNEFKSTEMEVHELSRHLTRFHRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.2418
R free: 0.2714
Average B factor: 41.03
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 0.2M Potassium Citrate
Matthews coefficient: 2.69
Solvent content (%): 54.23
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2020-09-30
Crystal structure of L-Trp/Indoleamine 2,3-dioxygenagse 1 (hIDO1) complex with the JK-loop refined in the closed conformation (PDB entry 7NGE)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 405 residues
Sequence: MGSSHHHHHHSSGSAAYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSAALELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.215
R free: 0.2707
Average B factor: 54.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 15.4% PEG 3350 
0.1M Phosphate buffer pH 6.0
Protein : 5mM HEPES pH 7.4, 200mM NaCl, 5mM DTT
Matthews coefficient: 3.04
Solvent content (%): 59.59
Ligand: TRYPTOPHAN (TRP)
Ligand formula: C11 H12 N2 O2
Ligand molecular weight: 204.225
Ligand SMILES: c1ccc2c(c1)c(c[nH]2)CC(C(=O)O)N
Ligand InChI: InChI=1S/C11H12N2O2/c12-9(11(14)15)5-7-6-13-10-4-2-1-3-8(7)10/h1-4,6,9,13H,5,12H2,(H,14,15)/t9-/m0/s1
Release date: 2021-12-29
HDAC6 ZnF domain inhibitor - DARPin (Designed Ankyrin repeat protein) F10 (PDB entry 7ZYU)
Macromolecule: Histone deacetylase 6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 110 residues
Sequence: GPTPLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFGEDMPHPH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.2166
R free: 0.2498
Average B factor: 78.11
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 3.6 M sodium formate, Bis-Tris 0.1M pH=6.7, 10% w/v Glycerol, 30% w/v 1,8-Diaminooctane(additive).
Matthews coefficient: 3.35
Solvent content (%): 63.29
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: 2022-06-01
Crystal structure of human Protein kinase CK2 catalytic subunit in complex with the ATP-competitive, tight-binding dibenzofuran inhibitor TF107 (5) (PDB entry 5N9K)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 335 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.643
R work: 0.1638
R free: 0.1843
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: Prior to the crystallization the inhibitor was solubilized in 100 % DMSO in a concentration of 10 mM. Then, this inhibitor stock solution was mixed in a Ratio of 1:10 with human CK2alpha (construct 1-335; solved with a Protein concentration of 8-10 mg/ml in 500 mM sodium chloride, 25 mM Tris/HCl pH 8.5). 
After a short time of incubation this mixture were mixed with reservoir solution [32 % (w/v) PEG4000, 0.2 M ammonium acetate, 0.1 M citrate pH 5.6] in a ratio of 2.5:1. 3.5 microliter of this final mixture was then equilibrated against the reservoir solution. The crystal growth was induced by seeding with 150 nanoliter seed suspension after an equilibration time of two days.
Matthews coefficient: 1.96
Solvent content (%): 37.29
Ligand: 1,3-bis(chloranyl)-6-[(~{E})-(4-methoxyphenyl)iminomethyl]dibenzofuran-2,7-diol (8QK)
Ligand formula: C20 H13 Cl2 N O4
Ligand molecular weight: 402.228
Ligand SMILES: COc1ccc(cc1)N=Cc2c(ccc3c2oc4c3c(c(c(c4)Cl)O)Cl)O
Ligand InChI: InChI=1S/C20H13Cl2NO4/c1-26-11-4-2-10(3-5-11)23-9-13-15(24)7-6-12-17-16(27-20(12)13)8-14(21)19(25)18(17)22/h2-9,24-25H,1H3/b23-9+
Release date: 2018-02-28
Crystal structure of human KDM4A in complex with compound 17f (PDB entry 6H4R)
Macromolecule: Lysine-specific demethylase 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 360 residues
Sequence: SMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.179
R free: 0.219
Average B factor: 55.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
Matthews coefficient: 2.47
Solvent content (%): 50.18
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: 2019-06-12
Crystal structure of c-MET bound by compound 8 (PDB entry 7B42)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: GNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.202
R free: 0.225
Average B factor: 39.8
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25 % PEG3350, 0.2 M MgCl2, 0.1 M bis-tris pH 6.5
Matthews coefficient: 2.62
Solvent content (%): 53.02
Ligand: 3-[(3-fluorophenyl)methyl]-5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridine (SW8)
Ligand formula: C22 H22 F N5
Ligand molecular weight: 375.442
Ligand SMILES: c1cc(cc(c1)F)Cc2c[nH]c3c2cc(cn3)c4cnn(c4)C5CCNCC5
Ligand InChI: InChI=1S/C22H22FN5/c23-19-3-1-2-15(9-19)8-17-12-26-22-21(17)10-16(11-25-22)18-13-27-28(14-18)20-4-6-24-7-5-20/h1-3,9-14,20,24H,4-8H2,(H,25,26)
Release date: 2020-12-09
Crystal structure of 2-mercapto-4-methylphenol bound to human carbonic anhydrase II (PDB entry 4Q99)
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): 1.5
R work: 0.16398
R free: 0.19229
Average B factor: 10.959
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, temperature 291K
Matthews coefficient: 2.07
Solvent content (%): 40.45
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: 2015-03-11
Crystal Structure of Drosophila DHX36 helicase in complex with polyT (PDB entry 5N8S)
Macromolecule: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: TTTTTTTTTTTTTTTT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.88
R work: 0.2073
R free: 0.2847
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MES monohydrate-imidazole
20mM sodium formate
20mM ammonium acetate
20mM sodium citrate tribasic hydrate
20mM sodium oxamate
20mM potassium sodium tartrate tetrahydrate
Matthews coefficient: 2.69
Solvent content (%): 54.3
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: 2018-03-14
Crystal structure of point mutated DUSP19 (I187A) (PDB entry 4D3R)
Macromolecule: DUAL SPECIFICITY PROTEIN PHOSPHATASE 19
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 140 residues
Sequence: QVGVIKPWLLLGSQDAAHDLDTLKKNKVTHILNVAYGVENAFLSDFTYKSISILDLPETNILSYFPECFEFIEEAKRKDGVVLVHSNAGVSRAAAIVIGFLMNSEQTSFTSAFSLVKNARPSACPNSGFMEQLRTYQEGK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.16091
R free: 0.19905
Average B factor: 16.567
Crystal growth procedure: 1.9M AMMONIUM SULFATE
Matthews coefficient: 2.18
Solvent content (%): 43.52
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: 2015-11-04
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z68299550 (PDB entry 5RXO)
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): 1.71
R work: 0.1723
R free: 0.2071
Average B factor: 21.472
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 (%): 40.99
Ligand: 3-chloro-N-(1-hydroxy-2-methylpropan-2-yl)benzamide (JOV)
Ligand formula: C11 H14 Cl N O2
Ligand molecular weight: 227.687
Ligand SMILES: CC(C)(CO)NC(=O)c1cccc(c1)Cl
Ligand InChI: InChI=1S/C11H14ClNO2/c1-11(2,7-14)13-10(15)8-4-3-5-9(12)6-8/h3-6,14H,7H2,1-2H3,(H,13,15)
Release date: 2020-11-11
TB19 complex (PDB entry 6VC9)
Macromolecule: TB19 heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 233 residues
Sequence: QEQLQESGPGLVKPSETLSLTCTVSGGSIRNNYYNWIRQPAGKGLEWIGRIYISGTTNSNPSLKSRVTMSIDTSKNQFSLKLSSVTAADTAIYYCAREHYVSGTSLDNWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTHHHHHH
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2366
R free: 0.2785
Average B factor: 60.829
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M sodium potassium phosphate pH 6.2, 35% 5-methyl-2,4-pentanediol, and 2.5% pentaerythritol ethoxylate
Matthews coefficient: 3.02
Solvent content (%): 59.3
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2020-11-11
Crystal structure of the phosphatidylinositol 4-kinase IIbeta (PDB entry 4WTV)
Macromolecule: Phosphatidylinositol 4-kinase type 2-beta,Endolysin,Phosphatidylinositol 4-kinase type 2-beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.67
Sequence length: 514 residues
Sequence: VTIGTSEMNAFLDDPEFADIMLRAEQAIEVGIFPERISQGSSGSYFVKDPKRKIIGVFKPKSEEPYGQLNPKWTKYNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNLGRGCLIPNQGYLSEAGAYLVDNKLHLSIVPKTKVVWLVSETFNYNAIDRAKSRGKKYALEKVPKVGRKFHRIGLPPKIGSFQLFVEGYKEAEYWLRKFEADPLPENIRKQFQSQFERLVILDYIIRNTDRGNDNWLVRYEKQKCEKEIDHKESKWIDDEEFLIKIAAIDNGLAFPFKHPDEWRAYPFHWAWLPQAKVPFSEEIRNLILPYISDMNFVQDLCEDLYELFKTDKGFDKATFESQMSVMRGQILNLTQALRDGKSPFQLVQIPCVIVE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.2088
R free: 0.2404
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM MES/Imidazole pH = 6.5, 10% w/v PEG 4000, 20% v/v glycerol, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol
Matthews coefficient: 2.61
Solvent content (%): 52.8
Ligand: ADENOSINE-5'-TRIPHOSPHATE (ATP)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2015-07-15
Crystal structure of human carbonic anhydrase II in complex with hydroxylamine-O-sulfonamide, a molecule incorporating two zinc-binding groups. (PDB entry 4YVY)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 259 residues
Sequence: SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.162
R free: 0.192
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate and 0.1 M Tris-HCl, pH 8.5
Matthews coefficient: 2.09
Solvent content (%): 41.19
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: 2016-03-30