satarupa22/MacromolecularLigandDB huggingface dataset:
Structure of Human Leukotriene A4 Hydrolase in complex with inhibitor H1 (PDB entry 4R7L)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 631 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPDVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.15251
R free: 0.18546
Average B factor: 18.01
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 6.8
Crystallization temperature (K): 277
Crystal growth procedure: 15% PEG 8000, 0.1mM Na-acetate, 0.1mM Imidazole, 5mM YbCL3, pH 6.8, VAPOR DIFFUSION, temperature 277K
Matthews coefficient: 2.36
Solvent content (%): 47.79
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: 2015-11-25
Crystal structure of DAPK1 in complex with quercetin. (PDB entry 5AUW)
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): 1.5
R work: 0.1885
R free: 0.2112
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 2 M ammonium sulfate, 0.1 M MES
Matthews coefficient: 1.91
Solvent content (%): 35.45
Ligand: 3,5,7,3',4'-PENTAHYDROXYFLAVONE (QUE)
Ligand formula: C15 H10 O7
Ligand molecular weight: 302.236
Ligand SMILES: c1cc(c(cc1C2=C(C(=O)c3c(cc(cc3O2)O)O)O)O)O
Ligand InChI: InChI=1S/C15H10O7/c16-7-4-10(19)12-11(5-7)22-15(14(21)13(12)20)6-1-2-8(17)9(18)3-6/h1-5,16-19,21H
Release date: 2015-10-07
The FK1 domain of FKBP51 in complex with SAFit-analog 15h (PDB entry 9EU8)
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): 2.3
R work: 0.2328
R free: 0.2595
Average B factor: 54.53
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 12% PEG3350, 0.2M ammonium acetate, 0.1M HEPES-NaOH pH 7.5
Matthews coefficient: 2.24
Solvent content (%): 44.99
Ligand: (4-methyl-1,3-thiazol-5-yl)methyl (2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate (A1H7B)
Ligand formula: C28 H38 N2 O6 S
Ligand molecular weight: 530.676
Ligand SMILES: Cc1c(scn1)COC(=O)C2CCCCN2C(=O)C(c3cc(c(c(c3)OC)OC)OC)C4CCCCC4
Ligand InChI: InChI=1S/C28H38N2O6S/c1-18-24(37-17-29-18)16-36-28(32)21-12-8-9-13-30(21)27(31)25(19-10-6-5-7-11-19)20-14-22(33-2)26(35-4)23(15-20)34-3/h14-15,17,19,21,25H,5-13,16H2,1-4H3/t21-,25-/m0/s1
Release date: 2024-06-12
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2940170964 (PDB entry 5RY1)
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): 1.52
R work: 0.2236
R free: 0.2528
Average B factor: 15.482
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: 2.05
Solvent content (%): 40.06
Ligand: (3R)-1-methylpiperidin-3-yl furan-2-carboxylate (WO1)
Ligand formula: C11 H15 N O3
Ligand molecular weight: 209.242
Ligand SMILES: CN1CCCC(C1)OC(=O)c2ccco2
Ligand InChI: InChI=1S/C11H15NO3/c1-12-6-2-4-9(8-12)15-11(13)10-5-3-7-14-10/h3,5,7,9H,2,4,6,8H2,1H3/t9-/m1/s1
Release date: 2020-11-11
Crystal Structure Of Aldose Reductase (AKR1B1) Complexed With NADP+ And AT-007 (PDB entry 8FH9)
Macromolecule: Aldo-keto reductase family 1 member B1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.300
Sequence length: 316 residues
Sequence: MASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIVSKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDEGLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDPSLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCALLSCTSHKDYPFHEEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1501
R free: 0.1818
Average B factor: 16.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 25%
PEG 3,350, 100 mM Bis-Tris
Matthews coefficient: 2.19
Solvent content (%): 43.9
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2023-12-20
TrkA JM-kinase with 2-fluoro-{N}-[2-(4-fluorophenyl)-6-methyl-3-pyridyl]-4-(trifluoromethyl)benzamide (PDB entry 5KMK)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: SSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.2238
R free: 0.2805
Average B factor: 57.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
Matthews coefficient: 2.38
Solvent content (%): 48.39
Ligand: 2-fluoranyl-~{N}-[2-(4-fluorophenyl)-6-methyl-pyridin-3-yl]-4-(trifluoromethyl)benzamide (6UG)
Ligand formula: C20 H13 F5 N2 O
Ligand molecular weight: 392.322
Ligand SMILES: Cc1ccc(c(n1)c2ccc(cc2)F)NC(=O)c3ccc(cc3F)C(F)(F)F
Ligand InChI: InChI=1S/C20H13F5N2O/c1-11-2-9-17(18(26-11)12-3-6-14(21)7-4-12)27-19(28)15-8-5-13(10-16(15)22)20(23,24)25/h2-10H,1H3,(H,27,28)
Release date: 2016-12-28
crystal structure of PDE5 in complex with a non-competitive inhibitor (PDB entry 6VBI)
Macromolecule: cGMP-specific 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 325 residues
Sequence: EETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.30000752706
R work: 0.189212588836
R free: 0.252496556648
Average B factor: 29.4860807999
Crystallization method: EVAPORATION
Crystallization temperature (K): 298
Crystal growth procedure: 8% PEG3350, 0.2 M ammonium acetate, 0.1 M Na Acetate, pH 4.6
Matthews coefficient: 2.51
Solvent content (%): 51.07
Ligand: (13bS)-4,9-dimethoxy-14-methyl-8,13,13b,14-tetrahydroindolo[2',3':3,4]pyrido[2,1-b]quinazolin-5(7H)-one (FZA)
Ligand formula: C21 H21 N3 O3
Ligand molecular weight: 363.41
Ligand SMILES: CN1c2cccc(c2C(=O)N3C1c4c(c5c([nH]4)cccc5OC)CC3)OC
Ligand InChI: InChI=1S/C21H21N3O3/c1-23-14-7-5-9-16(27-3)18(14)21(25)24-11-10-12-17-13(22-19(12)20(23)24)6-4-8-15(17)26-2/h4-9,20,22H,10-11H2,1-3H3/t20-/m0/s1
Release date: 2021-01-20
Human PTPRZ D1 domain complexed with NAZ2329 (PDB entry 5H08)
Macromolecule: Receptor-type tyrosine-protein phosphatase zeta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 298 residues
Sequence: GPAIPIKHFPKHVADLHASSGFTEEFEEVQSCTVDLGITADSSNHPDNKHKNRYINIVAYDHSRVKLAQLAEKDGKLTDYINANYVDGYNRPKAYIAAQGPLKSTAEDFWRMIWEHNVEVIVMITNLVEKGRRKCDQYWPADGSEEYGNFLVTQKSVQVLAYYTVRNFTLRNTKIKKGSQKGRPSGRVVTQYHYTQWPDMGVPEYSLPVLTFVRKAAYAKRHAVGPVVVHCSAGVGRTGTYIVLDSMLQQIQHEGTVNIFGFLKHIRSQRNYLVQTEEQYVFIHDTLVEAILSKETEV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.53
R work: 0.21029
R free: 0.29689
Average B factor: 39.25
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 10%(w/v) PEG8000, 20%(v/v) ethylene glycol, 30mM sodium fluoride, 30mM sodium bromide, 30mM sodium iodide. NAZ2329 was soaked into the crystal.
Matthews coefficient: 2.6
Solvent content (%): 52.68
Ligand: 3-{[2-Ethoxy-5-(trifluoromethyl)benzyl]sulfanyl}-N-(phenylsulfonyl)thiophene-2-carboxamide (7WL)
Ligand formula: C21 H18 F3 N O4 S3
Ligand molecular weight: 501.562
Ligand SMILES: CCOc1ccc(cc1CSc2ccsc2C(=O)NS(=O)(=O)c3ccccc3)C(F)(F)F
Ligand InChI: InChI=1S/C21H18F3NO4S3/c1-2-29-17-9-8-15(21(22,23)24)12-14(17)13-31-18-10-11-30-19(18)20(26)25-32(27,28)16-6-4-3-5-7-16/h3-12H,2,13H2,1H3,(H,25,26)
Release date: 2017-07-26
Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-glucose and NADH bound (PDB entry 6C5Z)
Macromolecule: UDP-glucose 6-dehydrogenase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1.22
Sequence length: 494 residues
Sequence: MFEIKKICCIGAGYVGGPTCSVIAHMCPEIRVTVVDVNESRINAWNSPTLPIYEPGLKEVVESCRGKNLFFSTNIDDAIKEADLVFISVNTPTKTYGMGKGRAADLKYIEACARRIVQNSNGYKIVTEKSTVPVRAAESIRRIFDANTKPNLNLQVLSNPEFLAEGTAIKDLKNPDRVLIGGDETPEGQRAVQALCAVYEHWVPREKILTTNTWSSELSKLAANLFLAQRISSINSISALCEATGADVEEVATAIGMDQRIGNKFLKASVGFGGSCFQKDVLNLVYLCEALNLPEVARYWQQVIDMNDYQRRRFASRIIDSLFNTVTDKKIAILGFAFKKDTGDTRESSSIYISKYLMDEGAHLHIYDPKVPREQIVVDLSHPGVSEDDQVSRLVTISKDPYEACDGAHAVVICTEWDMFKELDYERIHKKMLKPAFIFDGRRVLDGLHNELQTIGFQIETIGKKVSSKRIPYAPSGEIPKFSLQDPPNKKPKV
Oligomeric state: Hetero 6-mer
Stoichiometry: A5, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.2032
R free: 0.2589
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.8
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG3350, 50 mM dipotassium phosphate, 100 mM sodium glycine
Matthews coefficient: 2.84
Solvent content (%): 56.74
Ligand: URIDINE-5'-DIPHOSPHATE-GLUCOSE (UPG)
Ligand formula: C15 H24 N2 O17 P2
Ligand molecular weight: 566.302
Ligand SMILES: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
Ligand InChI: InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1
Release date: 2019-01-23
Structure of Phosphoinositide 3-kinase gamma (PI3K) bound to the potent inhibitor PIKin3 (PDB entry 5JHB)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 960 residues
Sequence: MSEESQAFQRQLTALIGYDVTDVSNVHDDELEFTRRGLVTPRMAEVASRDPKLYAMHPWVTSKPLPEYLWKKIANNCIFIVIHRSTTSQTIKVSPDDTPGAILQSFFTKMAKKKSLMDIPESQSEQDFVLRVCGRDEYLVGETPIKNFQWVRHCLKNGEEIHVVLDTPPDPALDEVRKEEWPLVDDCTGVTGYHEQLTIHGKDHESVFTVSLWDCDRKFRVKIRGIDIPVLPRNTDLTVFVEANIQHGQQVLCQRRTSPKPFTEEVLWNVWLEFSIKIKDLPKGALLNLQIYCGKAPALSSKASAESPSSESKGKVQLLYYVNLLLIDHRFLLRRGEYVLHMWQISGKGEDQGSFNADKLTSATNPDKENSMSISILLDNYCHPIALPKHQPTPDPEGDRVRAEMPNQLRKQLEAIIATDPLNPLTAEDKELLWHFRYESLKHPKAYPKLFSSVKWGQQEIVAKTYQLLARREVWDQSALDVGLTMQLLDCNFSDENVRAIAVQKLESLEDDDVLHYLLQLVQAVKFEPYHDSALARFLLKRGLRNKRIGHFLFWFLRSEIAQSRHYQQRFAVILEAYLRGCGTAMLHDFTQQVQVIEMLQKVTLDIKSLSAEKYDVSSQVISQLKQKLENLQNSQLPESFRVPYDPGLKAGALAIEKCKVMASKKKPLWLEFKCADPTALSNETIGIIFKHGDDLRQDMLILQILRIMESIWETESLDLCLLPYGCISTGDKIGMIEIVKDATTIAKIQQSTVGNTGAFKDEVLNHWLKEKSPTEEKFQAAVERFVYSCAGYCVATFVLGIGDRHNDNIMITETGNLFHIDFGHILGNYKSFLGINKERVPFVLTPDFLFVMGTSGKKTSPHFQKFQDICVKAYLALRHHTNLLIILFSMMLMTGMPQLTSKEDIEYIRDALTVGKNEEDAKKYFLDQIEVCRDKGWTVQFNWFLHLVLGIKQGEKHSA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.48
R work: 0.2307
R free: 0.2771
Average B factor: 102.0387
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 17%  PEG  4000,  250  mM  (NH4)2SO4 and  100mM  Tris  pH-7.5
Matthews coefficient: 2.32
Solvent content (%): 47.02
Ligand: [1-{4-[6-amino-4-(trifluoromethyl)pyridin-3-yl]-6-(morpholin-4-yl)-1,3,5-triazin-2-yl}-3-(chloromethyl)azetidin-3-yl]methanol (6K5)
Ligand formula: C18 H21 Cl F3 N7 O2
Ligand molecular weight: 459.853
Ligand SMILES: c1c(c(cnc1N)c2nc(nc(n2)N3CC(C3)(CO)CCl)N4CCOCC4)C(F)(F)F
Ligand InChI: InChI=1S/C18H21ClF3N7O2/c19-7-17(10-30)8-29(9-17)16-26-14(25-15(27-16)28-1-3-31-4-2-28)11-6-24-13(23)5-12(11)18(20,21)22/h5-6,30H,1-4,7-10H2,(H2,23,24)
Release date: 2017-03-15
Crystal structure of human LTA4H mutant D375N in complex with LTA4 (PDB entry 5NI6)
Macromolecule: Leukotriene A-4 hydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.6
Sequence length: 617 residues
Sequence: MHHHHHHPEIVDTCSLASPASVCRTKHLHLRCSVDFTRRTLTGTAALTVQSQEDNLRSLVLDTKDLTIEKVVINGQEVKYALGERQSYKGSPMEISLPIALSKNQEIVIEISFETSPKSSALQWLTPEQTSGKEHPYLFSQCQAIHCRAILPCQDTPSVKLTYTAEVSVPKELVALMSAIRDGETPDPEDPSRKIYKFIQKVPIPCYLIALVVGALESRQIGPRTLVWSEKEQVEKSAYEFSETESMLKIAEDLGGPYVWGQYDLLVLPPSFPYGGMENPCLTFVTPTLLAGDKSLSNVIAHEISHSWTGNLVTNKTWDHFWLNEGHTVYLERHICGRLFGEKFRHFNALGGWGELQNSVKTFGETHPFTKLVVDLTDIDPNVAYSSVPYEKGFALLFYLEQLLGGPEIFLGFLKAYVEKFSYKSITTDDWKDFLYSYFKDKVDVLNQVDWNAWLYSPGLPPIKPNYDMTLTNACIALSQRWITAKEDDLNSFNATDLKDLSSHQLNEFLAQTLQRAPLPLGHIKRMQEVYNFNAINNSEIRFRWLRLCIQSKWEDAIPLALKMATEQGRMKFTRPLFKDLAAFDKSHDQAVRTYQEHKASMHPVTAMLVGKDLKVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.54
R work: 0.1581
R free: 0.1908
Crystallization method: LIQUID DIFFUSION
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 22% (w/v) PEG 8000, 100 mM imidazole pH 7.0, 100 mM sodium acetate, 5 mM YbCl3
Matthews coefficient: 2.46
Solvent content (%): 50
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: 2017-08-23
Crystal Structure of human cyclic GMP-AMP synthase in complex with 6-(2-chloro-4-methylphenyl)-3-phenylbenzimidazole-4-carboxylic acid (PDB entry 7FUQ)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.757
R work: 0.1854
R free: 0.2337
Average B factor: 44.107
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Matthews coefficient: 2.14
Solvent content (%): 42.54
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: 2024-02-21
Crystal Structure of Ephrin A2 (EphA2) Receptor Protein Kinase with Compound 3a (PDB entry 5NKE)
Macromolecule: Ephrin type-A receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 306 residues
Sequence: GDPNQAVLKFTTEIHPSCVTRQKVIGAGEFGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGLSRVLEDDPEATYTTSGGKIPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIRLPSTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.172
R free: 0.204
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 37.5% MPD/PEG1000/PEG3350 (MD), 0.3 M Amino Acids Mix (MD), 0.1 M Buffer System 3 (MD) pH8.5
Matthews coefficient: 1.98
Solvent content (%): 37.72
Ligand: 2-[[3-bromanyl-5-(piperidin-4-ylcarbamoyl)phenyl]amino]-~{N}-(2-chloranyl-6-methyl-phenyl)-1,3-thiazole-5-carboxamide (90B)
Ligand formula: C23 H23 Br Cl N5 O2 S
Ligand molecular weight: 548.883
Ligand SMILES: Cc1cccc(c1NC(=O)c2cnc(s2)Nc3cc(cc(c3)Br)C(=O)NC4CCNCC4)Cl
Ligand InChI: InChI=1S/C23H23BrClN5O2S/c1-13-3-2-4-18(25)20(13)30-22(32)19-12-27-23(33-19)29-17-10-14(9-15(24)11-17)21(31)28-16-5-7-26-8-6-16/h2-4,9-12,16,26H,5-8H2,1H3,(H,27,29)(H,28,31)(H,30,32)
Release date: 2017-06-07
The crystal structue of PDE10A complexed with 1i (PDB entry 6KO0)
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: 322 residues
Sequence: MSICTSEEWQGLMQFTLPVRLCKEIELFHFDIGPFENMWPGIFVYMVHRSCGTSCFELEKLCRFIMSVKKNYRRVPYHNWKHAVTVAHCMYAILQNNHTLFTDLERKGLLIACLCHDLDHRGFSNSYLQKFDHPLAALYSTSTMEQHHFSQTVSILQLEGHNIFSTLSSSEYEQVLEIIRKAIIATDLALYFGNRKQLEEMYQTGSLNLNNQSHRDRVIGLMMTACDLCSVTKLWPVTKLTANDIYAEFWAEGDEMKKLGIQPIPMMDRDKKDEVPQGQLGFYNAVAIPCYTTLTQILPPTEPLLKACRDNLSQWEKVIRGE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.60002905998
R work: 0.214819538269
R free: 0.327303176933
Average B factor: 30.0466415313
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Hepes (pH 7.5), 0.2 M MgCl2, 18% PEG 3350, 50 mM 2-mercaptoethanol
Matthews coefficient: 2.22
Solvent content (%): 44.48
Ligand: 3-[2-(5-methyl-1-phenyl-benzimidazol-2-yl)ethyl]chromen-4-one (DKU)
Ligand formula: C25 H20 N2 O2
Ligand molecular weight: 380.439
Ligand SMILES: Cc1ccc2c(c1)nc(n2c3ccccc3)CCC4=COc5ccccc5C4=O
Ligand InChI: InChI=1S/C25H20N2O2/c1-17-11-13-22-21(15-17)26-24(27(22)19-7-3-2-4-8-19)14-12-18-16-29-23-10-6-5-9-20(23)25(18)28/h2-11,13,15-16H,12,14H2,1H3
Release date: 2020-04-01
Human p70s6k1 with ruthenium-based inhibitor EM5 (PDB entry 4RLO)
Macromolecule: Ribosomal protein S6 kinase beta-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 288 residues
Sequence: KIRPECFELLRVLGKGGYGKVFQVRKVTGANTGKIFAMKVLKKAMIVRNAKDTAHTKAERNILEEVKHPFIVDLIYAFQTGGKLYLILEYLSGGELFMQLEREGIFMEDTACFYLAEISMALGHLHQKGIIYRDLKPENIMLNHQGHVKLTDFGLCKESIHDGTVTHTFCGTIEYMAPEILMRSGHNRAVDWWSLGALMYDMLTGAPPFTGENRKKTIDKILKCKLNLPPYLTQEARDLLKKLLKRNAASRLGAGPGDAGEVQAHPFFRHINWEELLARKVEPPFKPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.527
R work: 0.1915
R free: 0.2221
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 288
Crystal growth procedure: 0.1M Tris, 3.5M Sodium Formate, with staurosporine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Matthews coefficient: 3.27
Solvent content (%): 62.34
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: 2015-01-21
Ni- Carbonic Anhydrase II pH 11.0 20 atm CO2 (PDB entry 6LV8)
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): 1.2
R work: 0.1121
R free: 0.1364
Average B factor: 11.329
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 11
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.1
Solvent content (%): 41.41
Ligand: CARBON DIOXIDE (CO2)
Ligand formula: C O2
Ligand molecular weight: 44.01
Ligand SMILES: C(=O)=O
Ligand InChI: InChI=1S/CO2/c2-1-3
Release date: 2020-08-19
Human anionic trypsin after autoproteolysis at Arg122 (PDB entry 7Z9F)
Macromolecule: Trypsin-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.4
Sequence length: 99 residues
Sequence: IVGGYICEENSVPYQVSLNSGYHFCGGSLISEQWVVSAGHCYKSRIQVRLGEHNIEVLEGNEQFINAAKIIRHPKYNSRTLDNDILLIKLSSPAVINSR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.187
R free: 0.2186
Average B factor: 20.03
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 1 uL protein (15 mg/mL in 20 mM Hepes pH 7.4, 150 mM NaCl, 1 mM CaCl2) + 1 uL well solution (22% PEG 4000, 0.1 M Hepes pH 7.5, 0.1 M NaAc)
Matthews coefficient: 2.18
Solvent content (%): 43.62
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2022-06-29