satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of NLRP3 in complex with inhibitor NP3-562 (PDB entry 8RI2)
Macromolecule: NACHT, LRR and PYD domains-containing protein 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4
Sequence length: 550 residues
Sequence: GKMKKDYRKKYRKYVRSRFQCIEDRNARLGESVSLNKRYTRLRLIKEHRSQQEREQELLAIGKTKTCESPVSPIKMELLFDPDDEHSEPVHTVVFQGAAGIGKTILARKMMLDWASGTLYQDRFDYLFYIHCREVSLVTQRSLGDLIMSCCPDPNPPIHKIVRKPSRILFLMDGFDELQGAFDEHIGPLCTDWQKAERGDILLSSLIRKKLLPEASLLITTRPVALEKLQHLLDHPRHVEILGFSEAKRKEYFFKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIVCTGLKQQMESGKSLAQTSKTTTAVYVFFLSSLLQPRGGSQEHGLCAHLWGLCSLAADGIWNQKILFEESDLRNHGLQKADVSAFLRMNLFQKEVDCEKFYSFIHMTFQEFFAAMYYLLEEEKEGRTNVPGSRLKLPSRDVTVLLENYGKFEKGYLIFVVRFLFGLVNQERTSYLEKKLSCKISQQIRLELLKWIEVKAKAKKLQIQPSQLELFYCLYEMQEEDFVQRAMDYFPKIEINLSTRMDHMVSSFCIENCHRVESL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2242
R free: 0.2702
Average B factor: 84.07
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: protein: well = 1: 1
well: 1.94 M Ammonium citrate pH 7.0
protein: 7 mg/ml protein copurified with 1 uM inhibitor
Matthews coefficient: 2.79
Solvent content (%): 55.94
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: 2024-01-17
Crystal Structure of human phosphodiesterase 10 in complex with 4-(azetidine-1-carbonyl)-2-methyl-N-[3-(phenylcarbamoyl)phenyl]pyrazole-3-carboxamide (PDB entry 5SHJ)
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): 2.3
R work: 0.1887
R free: 0.2437
Average B factor: 37.947
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: 2.67
Solvent content (%): 54.01
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
Crystal structure of DAPK1 in complex with pterostilbene (PDB entry 8IE7)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 293 residues
Sequence: MTVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.849
R work: 0.179
R free: 0.2107
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG400, ammonium sulfate, Bis-tris pH 6.5
Matthews coefficient: 1.88
Solvent content (%): 34.72
Ligand: Pterostilbene (3RL)
Ligand formula: C16 H16 O3
Ligand molecular weight: 256.296
Ligand SMILES: COc1cc(cc(c1)OC)C=Cc2ccc(cc2)O
Ligand InChI: InChI=1S/C16H16O3/c1-18-15-9-13(10-16(11-15)19-2)4-3-12-5-7-14(17)8-6-12/h3-11,17H,1-2H3/b4-3+
Release date: 2023-05-24
Crystal structure of EphA3 in complex with 18-Crown-6 (PDB entry 6IN0)
Macromolecule: Ephrin type-A receptor 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 301 residues
Sequence: MAKELDATNISIDKVVGAGEFGEVCSGRLKLPSKKEISVAIKTLKVGYTEKQRRDFLGEASIMGQFDHPNIIRLEGVVTKSKPVMIVTEYMENGSLDSFLRKHDAQFTVIQLVGMLRGIASGMKYLSDMGYVHRDLAARNILINSNLVCKVSDFGLSRVLEDDPEAAYTTRGGKIPIRWTSPEAIAYRKFTSASDVWSYGIVLWEVMSYGERPYWEMSNQDVIKAVDEGYRLPPPMDCPAALYQLMLDCWQKDRNNRPKFEQIVSILDKLIRNPGSLKIITSAAARPSNLLLDLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.501
R work: 0.1947
R free: 0.2294
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 13% PEG2000 monomethyl ether, 0.1 M MES pH 6.5, 0.1 M sodium acetate
Matthews coefficient: 2.23
Solvent content (%): 44.96
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2019-10-30
Discovery of IRAK4 Inhibitor 41 (PDB entry 8BR5)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 299 residues
Sequence: DTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2146
R free: 0.2541
Average B factor: 57.762
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: none
Matthews coefficient: 2.77
Solvent content (%): 55.53
Ligand: ~{N}-[2,3-dimethyl-6-(1~{H}-pyrazol-5-yl)benzimidazol-5-yl]-6-(trifluoromethyl)pyridine-2-carboxamide (R73)
Ligand formula: C19 H15 F3 N6 O
Ligand molecular weight: 400.357
Ligand SMILES: Cc1nc2cc(c(cc2n1C)NC(=O)c3cccc(n3)C(F)(F)F)c4ccn[nH]4
Ligand InChI: InChI=1S/C19H15F3N6O/c1-10-24-15-8-11(12-6-7-23-27-12)14(9-16(15)28(10)2)26-18(29)13-4-3-5-17(25-13)19(20,21)22/h3-9H,1-2H3,(H,23,27)(H,26,29)
Release date: 2024-01-31
6-substituted pyrrolo[2,3-d]pyrimidine 6-thieno-(4-methoxyphenyl) (PDB entry 5HT4)
Macromolecule: Dihydrofolate reductase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.5.1.3
Sequence length: 186 residues
Sequence: VGSLNCIVAVSQNMGIGKNGDLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINLVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHLKLFVTRIMQDFESDTFFPEIDLEKYKLLPEYPGVLSDVQEEKGIKYKFEVYEKND
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.24209
R free: 0.30437
Average B factor: 28.158
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 283
Crystal growth procedure: 100 mM KSO4, 60% sat AmSO4, 3%ETOH
Matthews coefficient: 2.55
Solvent content (%): 51.74
Ligand: 7-ethyl-6-[(3-methoxyphenyl)sulfanyl]-5-methyl-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine (65J)
Ligand formula: C16 H19 N5 O S
Ligand molecular weight: 329.42
Ligand SMILES: CCn1c2c(c(c1Sc3cccc(c3)OC)C)c(nc(n2)N)N
Ligand InChI: InChI=1S/C16H19N5OS/c1-4-21-14-12(13(17)19-16(18)20-14)9(2)15(21)23-11-7-5-6-10(8-11)22-3/h5-8H,4H2,1-3H3,(H4,17,18,19,20)
Release date: 2017-02-01
Crystal structure of 1-hydroxy-4-methylpyridin-2(1H)-one bound to human carbonic anhydrase II (PDB entry 4Q8Z)
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: 0.15298
R free: 0.17681
Average B factor: 12.084
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: MERCURIBENZOIC ACID (MBO)
Ligand formula: C7 H5 Hg O2
Ligand molecular weight: 321.703
Ligand SMILES: c1cc(ccc1C(=O)O)[Hg]
Ligand InChI: InChI=1S/C7H5O2.Hg/c8-7(9)6-4-2-1-3-5-6;/h2-5H,(H,8,9);
Release date: 2015-03-11
Crystal structure of the ACVR1 (ALK2) kinase in complex with the compound M4K2009 (PDB entry 6SZM)
Macromolecule: Activin receptor type I
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.1519
R free: 0.1883
Average B factor: 24.18
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 2M ammonium sulfate, 0.1M bis-tris pH 5.5
Matthews coefficient: 2.66
Solvent content (%): 53.81
Ligand: 1-[4-[4-methyl-5-(3,4,5-trimethoxyphenyl)pyridin-3-yl]phenyl]piperazine (M2Z)
Ligand formula: C25 H29 N3 O3
Ligand molecular weight: 419.516
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)N4CCNCC4
Ligand InChI: InChI=1S/C25H29N3O3/c1-17-21(18-5-7-20(8-6-18)28-11-9-26-10-12-28)15-27-16-22(17)19-13-23(29-2)25(31-4)24(14-19)30-3/h5-8,13-16,26H,9-12H2,1-4H3
Release date: 2019-10-16
MALT1(329-728) in complex with a sulfonamide containing compound (PDB entry 6YN9)
Macromolecule: Mucosa-associated lymphoid tissue lymphoma translocation protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22
Sequence length: 404 residues
Sequence: GPGSDNKEQTTDQPLAKDKVALLIGNMNYREHPKLKAPLVDVYELTNLLRQLDFKVVSLLDLTEYEMRNAVDEFLLLLDKGVYGLLYYAGHGYENFGNSFMVPVDAPNPYRSENCLCVQNILKLMQEKETGLNVFLLDMCRKRNDYDDTIPILDALKVTANIVFGYATCQGAEAFEIQHSGLANGIFMKFLKDRLLEDKKITVLLDEVAEDMGKCHLTKGKQALEIRSSLSEKRALTDPIQGTEYSAESLVRNLQWAKAHELPESMCLKFDCGVQIQLGFAAEFSNVMIIYTSIVYKPPEIIMCDAYVTDFPLDLDIDPKDANKGTPEETGSYLVSKDLPKHCLYTRLSSLQKLKEHLVFTVCLSYQYSGLEDTVEDKQEVNVGKPLIAKLDMHRGLGRKTCFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.558
R work: 0.2015
R free: 0.2512
Average B factor: 44.56
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 25% PEG MME 2000, 0.1M MES pH6.5
Protein at 12 mg/ml in 25mM HEPES pH 7.5, 50mM NaCl, 1mM TCEP, 100 mM Mg formate added prior to crystallization
Matthews coefficient: 2.03
Solvent content (%): 39.48
Ligand: 5-[4-[(2,6-diethylphenyl)sulfamoyl]-3-methyl-phenyl]furan-3-carboxylic acid (OZQ)
Ligand formula: C22 H23 N O5 S
Ligand molecular weight: 413.487
Ligand SMILES: CCc1cccc(c1NS(=O)(=O)c2ccc(cc2C)c3cc(co3)C(=O)O)CC
Ligand InChI: InChI=1S/C22H23NO5S/c1-4-15-7-6-8-16(5-2)21(15)23-29(26,27)20-10-9-17(11-14(20)3)19-12-18(13-28-19)22(24)25/h6-13,23H,4-5H2,1-3H3,(H,24,25)
Release date: 2020-06-24
TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid (PDB entry 5F03)
Macromolecule: Tryptase beta-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.59
Sequence length: 245 residues
Sequence: IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPKKP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.15494
R free: 0.20026
Average B factor: 15.628
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 10000, 0.1 M HEPES
Matthews coefficient: 2.67
Solvent content (%): 53.99
Ligand: (5~{S})-5-[[3-(aminomethyl)phenoxy]methyl]-3-[3-[2-(2-chloranylpyridin-3-yl)ethynyl]phenyl]-1,3-oxazolidin-2-one (5TA)
Ligand formula: C24 H20 Cl N3 O3
Ligand molecular weight: 433.887
Ligand SMILES: c1cc(cc(c1)OCC2CN(C(=O)O2)c3cccc(c3)C#Cc4cccnc4Cl)CN
Ligand InChI: InChI=1S/C24H20ClN3O3/c25-23-19(6-3-11-27-23)10-9-17-4-1-7-20(12-17)28-15-22(31-24(28)29)16-30-21-8-2-5-18(13-21)14-26/h1-8,11-13,22H,14-16,26H2/t22-/m0/s1
Release date: 2016-02-24
Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal peptide (PDB entry 6HKS)
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): 2.19441072073
R work: 0.194138416618
R free: 0.246797249095
Average B factor: 56.9100392383
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 20% w/v PEG 3350
0.2 mM KI
pH 7
Matthews coefficient: 3.47
Solvent content (%): 64.5
Ligand: IODIDE ION (IOD)
Ligand formula: I
Ligand molecular weight: 126.904
Ligand SMILES: [I-]
Ligand InChI: InChI=1S/HI/h1H/p-1
Release date: 2019-05-22
Human Carbonic Anhydrase II in complex with 4-(2-hydroxyethyl)benzenesulfonamide (PDB entry 6RG5)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 265 residues
Sequence: GSPEFMSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.089
R work: 0.1109
R free: 0.1273
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: Ammonium sulfate 2.7 M, Tris 0.1 M, pH = 7.8, saturated with para-Chloromercuribenzenesulfonamide
Matthews coefficient: 2.07
Solvent content (%): 40.7
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: 2020-05-13
Human Carbonic Anhydrase II complexed with an inhibitor with a benzenesulfonamide group (1). (PDB entry 4YX4)
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): 1.01
R work: 0.1509
R free: 0.1703
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 2.5 uL of the protein solution (10 mg/ml hCAII in 50 mM Tris pH 7.8) were mixed with 2.5 uL of the well solution (2.7 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with p-chloromercurybenzoicacid) and placed as a hanging drop. Crystals appeared after several days. The crystals were soaked in 3.0 M (NH4)SO4, 100 mM Tris, pH 7.8, saturated with the inhibitor, for 1 day.
Matthews coefficient: 2.07
Solvent content (%): 40.58
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: 2016-02-03
Crystal structure of the human WNK2 CCT1 domain (PDB entry 6ELM)
Macromolecule: Serine/threonine-protein kinase WNK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 98 residues
Sequence: SMAEDTGVRVELAEEDHGRKSTIALRLWVEDPKKLKGKPKDNGAIEFTFDLEKETPDEVAQEMIESGFFHESDVKIVAKSIRDRVALIQWRRERIWPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.14
R work: 0.1383
R free: 0.1683
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG1000 -- 0.1M SPG pH 8.0
Matthews coefficient: 2.06
Solvent content (%): 40.3
Release date: 2017-12-20
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with compound_FMOPL000396a (PDB entry 5QFY)
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): 1.769
R work: 0.1843
R free: 0.2123
Average B factor: 39.9028
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: 3.32
Solvent content (%): 62.94
Ligand: 1-methyl-N-[(thiophen-2-yl)methyl]-1H-pyrazole-5-carboxamide (JO1)
Ligand formula: C10 H11 N3 O S
Ligand molecular weight: 221.279
Ligand SMILES: Cn1c(ccn1)C(=O)NCc2cccs2
Ligand InChI: InChI=1S/C10H11N3OS/c1-13-9(4-5-12-13)10(14)11-7-8-3-2-6-15-8/h2-6H,7H2,1H3,(H,11,14)
Release date: 2018-10-10
Crystal structure of ALKBH1 and 13h complex. (PDB entry 8K62)
Macromolecule: Nucleic acid dioxygenase ALKBH1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 389 residues
Sequence: MGKMAAAVGSVATLATEPGEDAFRKLFRFYRQSRPGTADLEGVIDFSAAHAARGKGPGAQKVIKSQLNVSSVSEQNAYRAGLQPVSKWQAYGLKGYPGFIFIPNPFLPGYQWHWVKQCLKLYSQKPNVCNLDKHMSKEETQDLWEQSKEFLRYKEATKRRPRSLLEKLRWVTVGYHYNWDSKKYSADHYTPFPSDLGFLSEQVAAACGFEDFRAEAGILNYYRLDSTLGIHVDRSELDHSKPLLSFSFGQSAIFLLGGLQRDEAPTAMFMHSGDIMIMSGFSRLLNHAVPRVLPNPEGEGLPHCLEAPLPAVLPRDSMVEPCSMEDWQVCASYLKTARVNMTVRQVLATDQNFPLEPIEDEKRDISTEGFCHLDDQNSEVKRARINPDS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.991
R work: 0.2043
R free: 0.2777
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 0.1M imidazole, pH7.0, 20% Polyrthylene glycol 6000
Matthews coefficient: 2.02
Solvent content (%): 39.03
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: 2024-07-31
CRYSTAL STRUCTURE OF HUMAN MONOGLYCERIDE LIPASE WITH COMPOUND LEI-515 (PDB entry 8AQF)
Macromolecule: Monoglyceride lipase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.23
Sequence length: 323 residues
Sequence: MGSSHHHHHHSSGENLYFQGMPEESSPRRTPQSIPYQDLPHLVNADGQYLFCRYWAPTGTPKALIFVSHGAGEHSGRYEELARMLMGLDLLVFAHDHVGHGQSEGERMVVSDFHVFVRDVLQHVDSMQKDYPGLPVFLLGHSMGGAIAILTAAERPGHFAGMVLISPLVLANPESATTFKVLAAKVLNSVLPNLSSGPIDSSVLSRNKTEVDIYNSDPLICRAGLKVCFGIQLLNAVSRVERALPKLTVPFLLLQGSADRLCDSKGAYLLMELAKSQDKTLKIYEGAYHVLHKELPEVTNSVFHEINMWVSQRTATAGTASPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1544
R free: 0.1781
Average B factor: 31.073
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES pH 6.5, 6 to 13% PEG MME5K, 12% isopropanol
Matthews coefficient: 2.49
Solvent content (%): 50.53
Ligand: 1-[(~{R})-[2-chloranyl-4-[(2~{S},3~{S})-4-(3-chlorophenyl)-2,3-dimethyl-piperazin-1-yl]carbonyl-phenyl]sulfinyl]-3,3-bis(fluoranyl)pentan-2-one (NUX)
Ligand formula: C24 H26 Cl2 F2 N2 O3 S
Ligand molecular weight: 531.443
Ligand SMILES: CCC(C(=O)CS(=O)c1ccc(cc1Cl)C(=O)N2CCN(C(C2C)C)c3cccc(c3)Cl)(F)F
Ligand InChI: InChI=1S/C24H26Cl2F2N2O3S/c1-4-24(27,28)22(31)14-34(33)21-9-8-17(12-20(21)26)23(32)30-11-10-29(15(2)16(30)3)19-7-5-6-18(25)13-19/h5-9,12-13,15-16H,4,10-11,14H2,1-3H3/t15-,16-,34+/m0/s1
Release date: 2023-08-23
Structure of BTK with RN486 (PDB entry 5P9G)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 279 residues
Sequence: GKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1775
R free: 0.2135
Average B factor: 26.58
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: PEG 3350, sodium actate, BisTrisPropane
Matthews coefficient: 2.23
Solvent content (%): 44.95
Ligand: 6-cyclopropyl-8-fluoranyl-2-[2-(hydroxymethyl)-3-[1-methyl-5-[[5-(4-methylpiperazin-1-yl)pyridin-2-yl]amino]-6-oxidanylidene-pyridin-3-yl]phenyl]isoquinolin-1-one (7G6)
Ligand formula: C35 H35 F N6 O3
Ligand molecular weight: 606.689
Ligand SMILES: CN1CCN(CC1)c2ccc(nc2)NC3=CC(=CN(C3=O)C)c4cccc(c4CO)N5C=Cc6cc(cc(c6C5=O)F)C7CC7
Ligand InChI: InChI=1S/C35H35FN6O3/c1-39-12-14-41(15-13-39)26-8-9-32(37-19-26)38-30-18-25(20-40(2)34(30)44)27-4-3-5-31(28(27)21-43)42-11-10-23-16-24(22-6-7-22)17-29(36)33(23)35(42)45/h3-5,8-11,16-20,22,43H,6-7,12-15,21H2,1-2H3,(H,37,38)
Release date: 2017-05-24
Crystal structure of human cathepsin D in complex with macrocyclic inhibitor 9 (PDB entry 6QCB)
Macromolecule: Cathepsin D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.5
Sequence length: 97 residues
Sequence: GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQ
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.16637
R free: 0.18977
Average B factor: 22.435
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 25 % PEG 3350
0.2 lithium sulphate
0.1 Bis-Tris pH 5.5
Matthews coefficient: 3.01
Solvent content (%): 59.08
Ligand: PHOSPHITE ION (PO3)
Ligand formula: O3 P
Ligand molecular weight: 78.972
Ligand SMILES: [O-][P-](=O)[O-]
Ligand InChI: InChI=1S/O3P/c1-4(2)3/q-3
Release date: 2020-01-29