satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human Angiotensin-1 converting enzyme N-domain in complex with Omapatrilat. (PDB entry 6H5X)
Macromolecule: Angiotensin-converting enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1
Sequence length: 629 residues
Sequence: LDPGLQPGQFSADEAGAQLFAQSYQSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQQFTDPQLRRIIGAVRTLGSANLPLAKRQQYNALLSQMSRIYSTAKVCLPNKTATCWSLDPDLTNILASSRSYAMLLFAWEGWHNAAGIPLKPLYEDFTALSNEAYKQDGFTDTGAYWRSWYNSPTFEDDLEHLYQQLEPLYLNLHAFVRRALHRRYGDRYINLRGPIPAHLLGDMWAQSWENIYDMVVPFPDKPNLDVTSTMLQQGWQATHMFRVAEEFFTSLELSPMPPEFWEGSMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTMDQLSTVHHEMGHIQYYLQYKDLPVSLRRGANPGFHEAIGDVLALSVSTPEHLHKIGLLDRVTNDTESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGRTPPSRYNFDWWYLRTKYQGICPPVTRNETHFDAGAKFHVPNVTPYIRYFVSFVLQFQFHEALCKEAGYEGPLHQCDIYRSTKAGAKLRKVLRAGSSRPWQEVLKDMVGLDALDAQPLLKYFQLVTQWLQEQNQQNGEVLGWPEYQWHPPLPDNYPEGIDLVTDEAEASKFVEEYDL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1644
R free: 0.2038
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M Tris/Bicine pH 8.5, 0.06 M Divalent Cations, 30% PEG550MME?PEG20000
Matthews coefficient: 2.84
Solvent content (%): 56.69
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: 2018-11-07
Structure of PIK3CA with covalent inhibitor 19 (PDB entry 7R9V)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 948 residues
Sequence: AGTMVGNREEKILNREIGFAIGMPVCEFDMVKDPEVQDFRRNILNVCKEAVDLRDLNSPHSRAMYVYPPNVESSPELPKHIYNKLDKGQIIVVIWVIVSPNNDKQKYTLKINHDCVPEQVIAEAIRKKTRSMLLSSEQLKLCVLEYQGKYILKVCGCDEYFLEKYPLSQYKYIRSCIMLGRMPNLMLMAKESLYSQLPMDCFTMPSYSRRISTATPYMNGETSTKSLWVINSALRIKILCATYVNVNIRDIDKIYVRTGIYHGGEPLCDNVNTQRVPCSNPRWNEWLNYDIYIPDLPRAARLCLSICSVKGRKGAKEEHCPLAWGNINLFDYTDTLVSGKMALNLWPVPHGLEDLLNPIGVTGSNPNKETPCLELEFDWFSSVVKFPDMSVIEEHANWSVSREAGFSYSHAGLSNRLARDNELRENDKEQLKAISTRDPLSEITEQEKDFLWSHRHYCVTIPEILPKLLLSVKWNSRDEVAQMYCLVKDWPPIKPEQAMELLDCNYPDPMVRGFAVRCLEKYLTDDKLSQYLIQLVQVLKYEQYLDNLLVRFLLKKALTNQRIGHFFFWHLKSEMHNKTVSQRFGLLLESYCRACGMYLKHLNRQVEAMEKLINLTDILKQEKKDETQKVQMKFLVEQMRRPDFMDALQGFLSPLNPAHQLGNLRLEECRIMSSAKRPLWLNWENPDIMSELLFQNNEIIFKNGDDLRQDMLTLQIIRIMENIWQNQGLDLRMLPYGCLSIGDCVGLIEVVRNSHTIMQIQCKGGLKGALQFNSHTLHQWLKDKNKGEIYDAAIDLFTRSCAGYCVATFILGIGDRHNSNIMVKDDGQLFHIDFGHFLDHKKKKFGYKRERVPFVLTQDFLIVISKGAQECTKTREFERFQEMCYKAYLAIRQHANLFINLFSMMLGSGMPELQSFDDIAYIRKTLALDKTEQEALEYFMKQMNDAHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.2526
R free: 0.2919
Average B factor: 114.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: PEG6000 8%, 0.6 M sodium formate, 0.1 M CHES pH 9.4, 5 mM TCEP
Matthews coefficient: 2.61
Solvent content (%): 52.83
Ligand: N-[2-(4-{4-[2-amino-4-(difluoromethyl)pyrimidin-5-yl]-6-(morpholin-4-yl)-1,3,5-triazin-2-yl}piperazin-1-yl)-2-oxoethyl]-1-(prop-2-enoyl)piperidine-4-carboxamide (2Q7)
Ligand formula: C27 H35 F2 N11 O4
Ligand molecular weight: 615.635
Ligand SMILES: C=CC(=O)N1CCC(CC1)C(=O)NCC(=O)N2CCN(CC2)c3nc(nc(n3)N4CCOCC4)c5cnc(nc5C(F)F)N
Ligand InChI: InChI=1S/C27H35F2N11O4/c1-2-19(41)37-5-3-17(4-6-37)24(43)31-16-20(42)38-7-9-39(10-8-38)26-34-23(18-15-32-25(30)33-21(18)22(28)29)35-27(36-26)40-11-13-44-14-12-40/h2,15,17,22H,1,3-14,16H2,(H,31,43)(H2,30,32,33)
Release date: 2022-04-06
Structure of human USPL1 in complex with SUMO2 (PDB entry 7P99)
Macromolecule: SUMO-specific isopeptidase USPL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22
Sequence length: 338 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSPLESKCTSFPQALCVQWKNAYALCWLDCILSALVHSEELKNTVTGLCSKEESIFWRLLTKYNQANTLLYTSQLSGVKDGDCKKLTSEIFAEIETCLNEVRDEIFISLQPQLRCTLGDMESPVFAFPLLLKLETHIEKLFLYSFSWDFECSQCGHQYQNRHMKSLVTFTNVIPEWHPLNAAHFGPCNNCNSKSQIRKMVLEKVSPIFMLHFVEGLPQNDLQHYAFHFEGCLYQITSVIQYRANNHFITWILDADGSWLECDDLKGPCSERHKKFEVPASEIHIVIWERKISQVTDKEAACLPLKK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1745
R free: 0.1974
Average B factor: 33.986
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 311
Crystal growth procedure: 0.2M Potassium thiocyanate, 0.1M Sodium Acetate pH 5.0, 8% PEG20000, 8% PEG500MME
Matthews coefficient: 1.89
Solvent content (%): 35.05
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: 2022-03-02
Aurora-A in complex with TACC3 (PDB entry 5ODT)
Macromolecule: Aurora kinase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 283 residues
Sequence: MESKKRQWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIANFGWSVHAPSSRRTTLAGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEANTYQETYKRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSSKPSNAQNKESASKQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.021
R work: 0.1778
R free: 0.2111
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 2 M Ammonium sulphate
Matthews coefficient: 2.82
Solvent content (%): 56.46
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: 2018-03-14
Crystal structure of TTBK2 in complex with VNG2.73 (compound 42) (PDB entry 7Q8Y)
Macromolecule: Tau-tubulin kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 300 residues
Sequence: SMSGGGEQPDILSVGILVKERWKVLRKIGGGGFGEIYDALDMLTRENVALKVESAQQPKQVLKMEVAVLKKLQGKDHVCRFIGCGRNDRFNYVVMQLQGRNLADLRRSQSRGTFTISTTLRLGRQILESIESIHSVGFLHRDIKPSNFAMGRFPSTCRKCYMLDFGLARQFTNSCGDVRPPRAVAGFRGTVRYASINAHRNREMGRHDDLWSLFYMLVEFVVGQLPWRKIKDKEQVGSIKERYDHRLMLKHLPPEFSIFLDHISSLDYFTKPDYQLLTSVFDNSIKTFGVIESDPFDWEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1777
R free: 0.2052
Average B factor: 19.081
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 1.6M Na/K phosphate pH 7, 5% Glycerol, 0.1M tris 7.5
Matthews coefficient: 2.8
Solvent content (%): 56.11
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: 2022-03-09
EGFR (L858R, T790M, V948R) in complex with 1-{(3R,4R)-3-[5-Chloro-2-(1-methyl-1H-pyrazol-4-ylamino)-7H-pyrrolo[2,3-d]pyrimidin-4-yloxymethyl]-4-methoxy-pyrrolidin-1-yl}propenone (PF-06459988) (PDB entry 5HG7)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMRKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.215
R free: 0.246
Average B factor: 24.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 286
Crystal growth procedure: 0.1 M (5.0 uL of stock 1.0 M) HEPES (pH 7.50), 0.2 M (2.5 uL of stock 4.0 M) Ammonium sulfate, 10.0 %v/v (5.0 uL of stock 100.0 %v/v) iso-propanol, 20.0 %w/v (20.0 uL of stock 50.0 %w/v) PEG 8000
Matthews coefficient: 1.85
Solvent content (%): 33.35
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2016-01-27
X-Ray Characterization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors (PDB entry 5OVR)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 305 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSRVLQAEELHEKALDPFLLQAEFFEIPMNFVDPKEYDIPGLVRKNRYKTILPNPHSRVCLTSPDPDDPLSSYINANYIRGYGGEEKVYIATQGPIVSTVADFWRMVWQEHTPIIVMITNIEEMNEKCTEYWPEEQVAYDGVEITVQKVIHTEDYRLRLISLKSGTEERGLKHYWFTSWPDQKTPDRAPPLLHLVREVEEAAQQEGPHCAPIIVHCSAGIGRTGCFIATSICCQQLRQEGVVDILKTTCQLRQDRGGMIQTCEQYQFVHHVMSLYEKQLSHQS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.2139
R free: 0.2906
Average B factor: 17.17
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 26-28% PEG3350, 0.1M Bis-Tris pH5.5, 0.2M Lithium sulfate
Matthews coefficient: 2.55
Solvent content (%): 51.84
Ligand: [(~{S})-[4-[3-[(~{R})-(3,4-dichlorophenyl)-oxidanyl-methyl]phenyl]phenyl]-oxidanyl-methyl]phosphonic acid (AXK)
Ligand formula: C20 H17 Cl2 O5 P
Ligand molecular weight: 439.226
Ligand SMILES: c1cc(cc(c1)C(c2ccc(c(c2)Cl)Cl)O)c3ccc(cc3)C(O)P(=O)(O)O
Ligand InChI: InChI=1S/C20H17Cl2O5P/c21-17-9-8-16(11-18(17)22)19(23)15-3-1-2-14(10-15)12-4-6-13(7-5-12)20(24)28(25,26)27/h1-11,19-20,23-24H,(H2,25,26,27)/t19-,20+/m1/s1
Release date: 2017-11-22
Structure of the ASK1 central regulatory region (PDB entry 5ULM)
Macromolecule: Mitogen-activated protein kinase kinase kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 393 residues
Sequence: GPGSQYFRESILNDIRKARNLYTGKELAAELARIRQRVDNIEVLTADIVINLLLSYRDIQDYDSIVKLVETLEKLPTFDLASHHHVKFHYAFALNRRNLPGDRAKALDIMIPMVQSEGQVASDMYCLVGRIYKDMFLDSNFTDTESRDHGASWFKKAFESEPTLQSGINYAVLLLAAGHQFESSFELRKVGVKLSSLLGKKGNLEKLQSYWEVGFFLGASVLANDHMRVIQASEKLFKLKTPAWYLKSIVETILIYKHFVKLTTEQPVAKQELVDFWMDFLVEATKTDVTVVRFPVLILEPTKIYQPSYLSINNEVEEKTISIWHVLPDDKKGIHEWNFSASSVRGVSISKFEERCCFLYVLHNSDDFQIYFCTELHCKKFFEMVNTITEEKG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.23335
R free: 0.26716
Average B factor: 30.648
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.6
Crystallization temperature (K): 290
Crystal growth procedure: 0.1 M Sodium Fluoride, 10 % PEG 3350,
Matthews coefficient: 2.34
Solvent content (%): 47.46
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2017-03-01
Structure of PP5C with LB-100; 7-oxabicyclo[2.2.1]heptane-2,3-dicarbonyl moiety modeled in the density (PDB entry 5WG8)
Macromolecule: Serine/threonine-protein phosphatase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.16
Sequence length: 333 residues
Sequence: GASMTIEDEYSGPKLEDGKVTISFMKELMQWYKDQKKLHRKCAYQILVQVKEVLSKLSTLVETTLKETEKITVCGDTHGQFYDLLNIFELNGLPSETNPYIFNGDFVDRGSFSVEVILTLFGFKLLYPDHFHLLRGNHETDNMNQIYGFEGEVKAKYTAQMYELFSEVFEWLPLAQCINGKVLIMHGGLFSEDGVTLDDIRKIERNRQPPDSGPMCDLLWSDPQPQNGRSISKRGVSCQFGPDVTKAFLEENNLDYIIRSHEVKAEGYEVAHGGRCVTVFSAPNYCDQMGNKASYIHLQGSDLRPQFHQFTAVPHPNVKPMAYANTLLQLGMM
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.1587
R free: 0.1961
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 289.15
Crystal growth procedure: 10 mM Tris-HCl pH 8.0, 35% 2-methyl-2,4-pentanediol, and 10% polyethylene glycol methyl ether 5000
Matthews coefficient: 2.43
Solvent content (%): 49.4
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: 2018-07-18
Crystal structure of PDE5A in complex with a novel inhibitor (PDB entry 8W4T)
Macromolecule: cGMP-specific 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 347 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.199
R work: 0.2202
R free: 0.2684
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris-HCl, 0.2 M MgSO4, 20% PEG 3350
Matthews coefficient: 2.66
Solvent content (%): 53.67
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2023-11-22
DNA Polymerase Mu Product Complex, 10 mM Mg2+ (960 min) (PDB entry 5TYG)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.726
R work: 0.1547
R free: 0.1853
Average B factor: 32.5416
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.67
Solvent content (%): 53.96
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2017-08-30
Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol) (PDB entry 5F6W)
Macromolecule: SUMO-conjugating enzyme UBC9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 157 residues
Sequence: SGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMNWECAIPGAAGTPWAGGLFKLRMLFKDDYPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYCQNRVEYEKRVRAQAKKFAPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.699
R work: 0.1718
R free: 0.2004
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol
Matthews coefficient: 2.73
Solvent content (%): 54.98
Ligand: 2-(2-hydroxyphenyl)phenol (5VL)
Ligand formula: C12 H10 O2
Ligand molecular weight: 186.207
Ligand SMILES: c1ccc(c(c1)c2ccccc2O)O
Ligand InChI: InChI=1S/C12H10O2/c13-11-7-3-1-5-9(11)10-6-2-4-8-12(10)14/h1-8,13-14H
Release date: 2016-04-27
BRAF in complex with N-(3-(2-(2-hydroxyethoxy)-6-morpholinopyridin-4-yl)-4-methylphenyl)-2-(trifluoromethyl)isonicotinamide (LXH254) (PDB entry 6N0P)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 273 residues
Sequence: DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.194
R free: 0.233
Average B factor: 39.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM Tris ph 7.7, 12% PEG8000, and 100 mM NaCl
Matthews coefficient: 2.95
Solvent content (%): 58.37
Ligand: N-{3-[2-(2-hydroxyethoxy)-6-(morpholin-4-yl)pyridin-4-yl]-4-methylphenyl}-2-(trifluoromethyl)pyridine-4-carboxamide (K81)
Ligand formula: C25 H25 F3 N4 O4
Ligand molecular weight: 502.486
Ligand SMILES: Cc1ccc(cc1c2cc(nc(c2)OCCO)N3CCOCC3)NC(=O)c4ccnc(c4)C(F)(F)F
Ligand InChI: InChI=1S/C25H25F3N4O4/c1-16-2-3-19(30-24(34)17-4-5-29-21(12-17)25(26,27)28)15-20(16)18-13-22(32-6-9-35-10-7-32)31-23(14-18)36-11-8-33/h2-5,12-15,33H,6-11H2,1H3,(H,30,34)
Release date: 2019-09-04
Crystal structure of human Integrator IntS9-IntS11 CTD complex (PDB entry 5V8W)
Macromolecule: Integrator complex subunit 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 78 residues
Sequence: MKPLLSGSIPVEQFVQTLEKHGFSDIKVEDTAKGHIVLLQEAETLIQIEEDSTHIICDNDEMLRVRLRDLVLKFLQKF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1665
R free: 0.2203
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Bis-Tris pH 6.5, 21-24% PEG 3350
Matthews coefficient: 2.39
Solvent content (%): 48.45
Release date: 2017-04-12
Crystal Structure of human phosphodiesterase 10 in complex with 2,3,5-trimethyl-6-[2-(1-methyl-4-phenylimidazol-2-yl)ethyl]pyrazine (PDB entry 5SEV)
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): 2.31
R work: 0.1789
R free: 0.2313
Average B factor: 49.231
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: 2.64
Solvent content (%): 53.42
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
Myotubularin-related proetin 1 (PDB entry 5C16)
Macromolecule: Myotubularin-related protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.64
Sequence length: 571 residues
Sequence: MEEAPLFPGESIKAIVKDVMYICPFMGAVSGTLTVTDFKLYFKNVERDPHFILDVPLGVISRVEKIGAQSHGDNSCGIEIVCKDMRNLRLAYKQEEQSKLGIFENLNKHAFPLSNGQALFAFSYKEKFPINGWKVYDPVSEYKRQGLPNESWKISKINSNYEFCDTYPAIIVVPTSVKDDDLSKVAAFRAKGRVPVLSWIHPESQATITRCSQPLVGPNDKRCKEDEKYLQTIMDANAQSHKLIIFDARQNSVADTNKTKGGGYESESAYPNAELVFLEIHNIHVMRESLRKLKEIVYPSIDEARWLSNVDGTHWLEYIRMLLAGAVRIADKIESGKTSVVVHSSDGWDRTAQLTSLAMLMLDSYYRTIKGFETLVEKEWISFGHRFALRVGHGNDNHADADRSPIFLQFVDCVWQMTRQFPSAFEFNELFLITILDHLYSCLFGTFLCNCEQQRFKEDVYTKTISLWSYINSQLDEFSNPFFVNYENHVLYPVASLSHLELWVNYYVRWNPRMRPQMPIHQNLKELLAVRAELQKRVEGLQREVATRAVSSSSERGSSPSHSATSVHTSV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.2203
R free: 0.2735
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: Sodium-HEPES, PEG 20000
Matthews coefficient: 2.36
Solvent content (%): 47.8
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: 2016-04-27
CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN IN COMPLEX WITH PHA-848125 (PDB entry 5VD1)
Macromolecule: Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 311 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMHQLQPRRVSFRGEASETLQSPGYDPSRPESFFQQSFQRLSRLGHGSYGEVFKVRSKEDGRLYAVKRSMSPFRGPKDRARKLAEVGSHEKVGQHPCCVRLEQAWEEGGILYLQTELCGPSLQQHCEAWGASLPEAQVWGYLRDTLLALAHLHSQGLVHLDVKPANIFLGPRGRCKLGDFGLLVELGTAGAGEVQEGDPRYMAPELLQGSYGTAADVFSLGLTILEVACNMELPHGGEGWQQLRQGYLPPEFTAGLSSELRSVLVMMLEPDPKLRATAEALLALPVLRQP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1465
R free: 0.1944
Average B factor: 28.1278
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 14 MG/ML MYT1, 50 mM HEPES PH 7.5, 0.5 mM DTT, 0.05 M POTASSIUM CHLORIDE, 17.5 (V/V) % pentaerythritol propoxylate (5/4 PO/OH), 1.5 mM PHA-848125
Matthews coefficient: 2.13
Solvent content (%): 42.16
Ligand: N,1,4,4-TETRAMETHYL-8-{[4-(4-METHYLPIPERAZIN-1-YL)PHENYL]AMINO}-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE (P48)
Ligand formula: C25 H32 N8 O
Ligand molecular weight: 460.575
Ligand SMILES: CC1(Cc2cnc(nc2-c3c1c(nn3C)C(=O)NC)Nc4ccc(cc4)N5CCN(CC5)C)C
Ligand InChI: InChI=1S/C25H32N8O/c1-25(2)14-16-15-27-24(29-20(16)22-19(25)21(23(34)26-3)30-32(22)5)28-17-6-8-18(9-7-17)33-12-10-31(4)11-13-33/h6-9,15H,10-14H2,1-5H3,(H,26,34)(H,27,28,29)
Release date: 2017-08-23
JAK2 JH1 in complex with Fedratinib (PDB entry 6VNE)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.32
R work: 0.2175
R free: 0.2563
Average B factor: 76.4045
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350
Matthews coefficient: 3.17
Solvent content (%): 61.23
Ligand: N-tert-butyl-3-{[5-methyl-2-({4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}amino)pyrimidin-4-yl]amino}benzenesulfonamide (2TA)
Ligand formula: C27 H36 N6 O3 S
Ligand molecular weight: 524.678
Ligand SMILES: Cc1cnc(nc1Nc2cccc(c2)S(=O)(=O)NC(C)(C)C)Nc3ccc(cc3)OCCN4CCCC4
Ligand InChI: InChI=1S/C27H36N6O3S/c1-20-19-28-26(30-21-10-12-23(13-11-21)36-17-16-33-14-5-6-15-33)31-25(20)29-22-8-7-9-24(18-22)37(34,35)32-27(2,3)4/h7-13,18-19,32H,5-6,14-17H2,1-4H3,(H2,28,29,30,31)
Release date: 2021-02-17