satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of PROTAC 5 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB (PDB entry 7Z6L)
Macromolecule: von Hippel-Lindau disease tumor suppressor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 162 residues
Sequence: GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD
Oligomeric state: Hetero 4-mer
Stoichiometry: A1, B1, C1, D1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.189
R free: 0.232
Average B factor: 52.75
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 33% (v/v) glycerol ethoxylate, 0.2 M ammonium chloride, 0.1 M HEPES, pH 7.5
Matthews coefficient: 2.15
Solvent content (%): 42.9
Ligand: (2~{S},4~{R})-~{N}-[[2-[3-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-benzimidazolo[1,2-a]quinazolin-9-yl)piperidin-1-yl]propoxy]-4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide (IEI)
Ligand formula: C53 H62 Br F N8 O6 S
Ligand molecular weight: 1038.077
Ligand SMILES: Cc1c(scn1)c2ccc(c(c2)OCCCN3CCC(CC3)c4ccc5c(c4)N(C6=NC(=O)c7c(cccc7Br)N56)C8CCCC8)CNC(=O)C9CC(CN9C(=O)C(C(C)(C)C)NC(=O)C1(CC1)F)O
Ligand InChI: InChI=1S/C53H62BrFN8O6S/c1-31-45(70-30-57-31)34-13-14-35(28-56-47(65)42-27-37(64)29-61(42)49(67)46(52(2,3)4)58-50(68)53(55)19-20-53)43(26-34)69-24-8-21-60-22-17-32(18-23-60)33-15-16-39-41(25-33)62(36-9-5-6-10-36)51-59-48(66)44-38(54)11-7-12-40(44)63(39)51/h7,11-16,25-26,30,32,36-37,42,46,64H,5-6,8-10,17-24,27-29H2,1-4H3,(H,56,65)(H,58,68)/t37-,42+,46-/m1/s1
Release date: 2022-09-07
Crystal structure of DAPK2 S308A Calcium/Calmodulin complex (PDB entry 6PAW)
Macromolecule: Death-associated protein kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 323 residues
Sequence: GHMSEPFKQQKVEDFYDIGEELGSGQFAIVKKCREKSTGLEYAAKFIKKRQSRASRRGVSREEIEREVSILRQVLHHNVITLHDVYENRTDVVLILELVSGGELFDFLAQKESLSEEEATSFIKQILDGVNYLHTKKIAHFDLKPENIMLLDKNIPIPHIKLIDFGLAHEIEDGVEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANITSVSYDFDEEFFSHTSELAKDFIRKLLVKETRKRLTIQEALRHPWITPVDNQQAMVRRESVVNLENFRKQYVRRRWKLAFSIVSLCNHLTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.953
R work: 0.2486
R free: 0.2884
Average B factor: 57.7375
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 292.15
Crystal growth procedure: 0.1 M Bis-Tris-HCl, pH 6.5, 0.6 M sodium chloride, 14.3% PEG3350
Matthews coefficient: 2.6
Solvent content (%): 52.73
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: 2020-06-17
Crystal structure of human USP2 C276S mutant in complex with ubiquitin (PDB entry 5XVE)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 356 residues
Sequence: MNSKSAQGLAGLRNLGNTSFMNSILQCLSNTRELRDYCLQRLYMRDLHHGSNAHTALVEEFAKLIQTIWTSSPNDVVSPSEFKTQIQRYAPRFVGYNQQDAQEFLRFLLDGLHNEVNRVTLRPKSNPENLDHLPDDEKGRQMWRKYLEREDSRIGDLFVGQLKSSLTCTDCGYCSTVFDPFWDLSLPIAKRGYPEVTLMDCMRLFTKEDVLDGDEKPTCCRCRGRKRCIKKFSIQRFPKILVLHLKRFSESRIRTSKLTTFVNFPLRDLDLREFASENTNHAVYNLYAVSNHSGTTMGGHYTAYCRSPGTGEWHTFNDSSVTPMSSSQVRTSDAYLLFYELASPPSRMLEHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.24
R work: 0.14694
R free: 0.16403
Average B factor: 15.025
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 295
Crystal growth procedure: 21% PEG3350, 8% Tacsimate (pH8.0)
Matthews coefficient: 1.98
Solvent content (%): 37.84
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: 2018-02-28
CDK2 IN COMPLEX WITH COMPOUND 4 (PDB entry 7RA5)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 300 residues
Sequence: GAMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.2252
R free: 0.2739
Average B factor: 28.64
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: PEG3350, MES pH 7
Matthews coefficient: 2.05
Solvent content (%): 39.93
Ligand: 4-[7-(methanesulfonyl)-1H-indol-3-yl]-N-[(3S)-piperidin-3-yl]-5-(trifluoromethyl)pyrimidin-2-amine (3I3)
Ligand formula: C19 H20 F3 N5 O2 S
Ligand molecular weight: 439.455
Ligand SMILES: CS(=O)(=O)c1cccc2c1[nH]cc2c3c(cnc(n3)NC4CCCNC4)C(F)(F)F
Ligand InChI: InChI=1S/C19H20F3N5O2S/c1-30(28,29)15-6-2-5-12-13(9-24-17(12)15)16-14(19(20,21)22)10-25-18(27-16)26-11-4-3-7-23-8-11/h2,5-6,9-11,23-24H,3-4,7-8H2,1H3,(H,25,26,27)/t11-/m0/s1
Release date: 2021-11-03
X-ray structure of furin (PCSK3) in complex with 1H-isoindol-3-amine (PDB entry 8B4W)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 480 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1659
R free: 0.179
Average B factor: 27.18
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL
Matthews coefficient: 3.75
Solvent content (%): 67.17
Ligand: 1H-isoindol-3-amine (F05)
Ligand formula: C8 H8 N2
Ligand molecular weight: 132.163
Ligand SMILES: c1ccc2c(c1)CN=C2N
Ligand InChI: InChI=1S/C8H8N2/c9-8-7-4-2-1-3-6(7)5-10-8/h1-4H,5H2,(H2,9,10)
Release date: 2023-10-04
Crystal structure of human JMJD2A in complex with compound 36 (PDB entry 5A7P)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 4A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 381 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFLKESEL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.1876
R free: 0.2362
Crystallization pH: 5.5
Crystal growth procedure: 28% PEG3350, 0.1M BIS-TRIS PH 5.5, 0.15M AMMONIUM SULFATE
Matthews coefficient: 2.66
Solvent content (%): 53.78
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: 2016-01-13
HRAS R97A Crystal Form 1 R-state (PDB entry 8ELS)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 189 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYAEQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.267
R work: 0.1622
R free: 0.2115
Average B factor: 35.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: PEG 3350,
Calcium Acetate,
HEPES,
Calcium Chloride,
Magnesium Chloride
Matthews coefficient: 2.41
Solvent content (%): 49.04
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2023-09-06
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1102357527 (PDB entry 7G84)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.811
R work: 0.1945
R free: 0.2322
Average B factor: 27.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.52
Solvent content (%): 51.25
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2023-07-12
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor A26 (PDB entry 7TGT)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: ANPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.06
R work: 0.1364
R free: 0.1447
Average B factor: 12.17
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 298
Crystal growth procedure: 29% PEG 3350
0.5 M KH2PO4
Protein and inhibitor were mixed in ratio 1:1.5
1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor
Matthews coefficient: 2.46
Solvent content (%): 50
Ligand: (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide (I4F)
Ligand formula: C41 H51 N7 O8
Ligand molecular weight: 769.886
Ligand SMILES: c1ccc(cc1)CC23CCCN(C2)C(=O)C=CC(=O)NCCC(NC(=O)Cc4ccccc4CNC(=O)C(NC3=O)Cc5ccco5)C(=O)NCCOCCN
Ligand InChI: InChI=1S/C41H51N7O8/c42-17-22-55-23-19-44-38(52)33-15-18-43-35(49)13-14-37(51)48-20-7-16-41(28-48,26-29-8-2-1-3-9-29)40(54)47-34(25-32-12-6-21-56-32)39(53)45-27-31-11-5-4-10-30(31)24-36(50)46-33/h1-6,8-14,21,33-34H,7,15-20,22-28,42H2,(H,43,49)(H,44,52)(H,45,53)(H,46,50)(H,47,54)/b14-13+/t33-,34-,41-/m0/s1
Release date: 2022-08-24
Structure of PARP2 catalytic domain bound to an isoindolinone inhibitor (PDB entry 4ZZX)
Macromolecule: POLY [ADP-RIBOSE] POLYMERASE 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 363 residues
Sequence: GPSLKSPLKPESQLDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAPPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNFLQLW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.21274
R free: 0.2441
Average B factor: 21.089
Crystallization temperature (K): 277
Crystal growth procedure: 25% PEG4000, 0.2M MAGNESIUM CHLORIDE, 0.1 M TRIS PH 8.5, 277K
Matthews coefficient: 2.2
Solvent content (%): 44.6
Ligand: 2-(3-methoxypropyl)-3-oxo-2,3-dihydro-1H-isoindole-4-carboxamide (FSU)
Ligand formula: C13 H16 N2 O3
Ligand molecular weight: 248.278
Ligand SMILES: COCCCN1Cc2cccc(c2C1=O)C(=O)N
Ligand InChI: InChI=1S/C13H16N2O3/c1-18-7-3-6-15-8-9-4-2-5-10(12(14)16)11(9)13(15)17/h2,4-5H,3,6-8H2,1H3,(H2,14,16)
Release date: 2015-08-12
CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU (PDB entry 5ABD)
Macromolecule: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 95 residues
Sequence: GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.995
R work: 0.1785
R free: 0.2216
Average B factor: 48.4
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: VAPOR DIFFUSION METHOD, MOTHER LIQUOR: 1.5MICROM VERGFR1-D2, 15MM TRIS/HCL PH 8.1, 25MM NACL, 5MM CUSO4 RESERVOIR: 19.5% (W/V) PEG8000, 100MM SA,
Matthews coefficient: 2.91
Solvent content (%): 57.75
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-09-28
Crystal structure of haspin (GSG2) in complex with macrocycle ODS2002941 (PDB entry 6Z5A)
Macromolecule: Serine/threonine-protein kinase haspin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 357 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMGECSQKGPVPFSHCLPTEKLQRCEKIGEGVFGEVFQTIADHTPVAIKIIAIEGPDLVNGSHQKTFEEILPEIIISKELSLLSGEVCNRTEGFIGLNSVHCVQGSYPPLLLKAWDHYNSTKGSANDRPDFFKDDQLFIVLEFEFGGIDLEQMRTKLSSLATAKSILHQLTASLAVAEASLRFEHRDLHWGNVLLKKTSLKKLHYTLNGKSSTIPSCGLQVSIIDYTLSRLERDGIVVFCDVSMDEDLFTGDGDYQFDIYRLMKKENNNRWGEYHPYSNVLWLHYLTDKMLKQMTFKTKCNTPAMKQIKRKIQEFHRTMLNFSSATDLLCQHSLFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1559
R free: 0.1822
Average B factor: 13.897
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277.15
Crystal growth procedure: 60.0% MPD, 0.1M SPG pH 6.0
Matthews coefficient: 3.11
Solvent content (%): 60.49
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: 2020-06-03
STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUND TETHERED WITH SRC CO-ACTIVATOR PEPTIDE AND COMPOUND-3 AKA 1,1,1,3,3,3-HEXAFLUORO-2-{4-[1-(4- LUOROBENZENESULFONYL)CYCLOPENTYL]PHENYL}PROPAN-2-OL (PDB entry 6NX1)
Macromolecule: Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 fusion
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 351 residues
Sequence: HHHHHHGSERTGTQPLGVQGLTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPGVLSSGCELPESLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQELFGITGSSGGSGGSSHSSLTERHKILHRLLQEGSPSDITTLSVEPD
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.27
R work: 0.2107
R free: 0.2397
Average B factor: 62.86
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 296
Crystal growth procedure: 0.1M Hepes pH 7.5, 150mM NaCl, 10-15%(V/V)PEG10K, Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen
Matthews coefficient: 2.51
Solvent content (%): 50.99
Ligand: 1,1,1,3,3,3-hexafluoro-2-(4-{1-[(4-fluorophenyl)sulfonyl]cyclopentyl}phenyl)propan-2-ol (L7D)
Ligand formula: C20 H17 F7 O3 S
Ligand molecular weight: 470.401
Ligand SMILES: c1cc(ccc1C2(CCCC2)S(=O)(=O)c3ccc(cc3)F)C(C(F)(F)F)(C(F)(F)F)O
Ligand InChI: InChI=1S/C20H17F7O3S/c21-15-7-9-16(10-8-15)31(29,30)17(11-1-2-12-17)13-3-5-14(6-4-13)18(28,19(22,23)24)20(25,26)27/h3-10,28H,1-2,11-12H2
Release date: 2020-02-12
Crystal structure of human PTPN2 catalytic domain (PDB entry 9C54)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 315 residues
Sequence: GMPTTIEREFEELDTQRRWQPLYLEIRNESHDYPHRVAKFPENRNRNRYRDVSPYDHSRVKLQNAENDYINASLVDIEEAQRSYILTQGPLPNTCCHFWLMVWQQKTKAVVMLNRIVEKESVKCAQYWPTDDQEMLFKETGFSVKLLSEDVKSYYTVHLLQLENINSGETRTISHFHYTTWPDFGVPESPASFLNFLFKVRESGSLNPDHGPAVIHCSAGIGRSGTFSLVDTCLVLMEKGDDINIKQVLLNMRKYRMGLIQTPDQLRFSYMAIIEGAKCIKGDSSIQKRWKELSKEDLSPAFDHSPNKIMTEKYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.1864
R free: 0.2352
Average B factor: 49.27
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 7% w/v PEG 8000, 14% v/v ethylene glycol, 25mM sodium l-glutamate, 25mM dl-alanine, 25mM glycine, 25mM dl-lysine HCl, 25mM dl-serine, 100mM MES/imidazole pH6.5
Matthews coefficient: 2.32
Solvent content (%): 47.06
Release date: 2024-09-04
C-terminal HsNMT1 deltaC3 truncation in complex with both MyrCoA and GNCFSKPR substrates (PDB entry 6SK3)
Macromolecule: Glycylpeptide N-tetradecanoyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.97
Sequence length: 399 residues
Sequence: GGSEFSVGQGPAKTMEEASKRSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2459
R free: 0.2686
Average B factor: 39.0239
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 293
Crystal growth procedure: 19% PEG6K, 100mM Sodium Citrate pH 5.6, 100mM MgCl2, 100mM NaCl.
Matthews coefficient: 2.1
Solvent content (%): 41.38
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: 2020-03-18
Crystal structure of Tdp1 catalytic domain in complex with compound XZ523 (PDB entry 6N0O)
Macromolecule: Tyrosyl-DNA phosphodiesterase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4
Sequence length: 461 residues
Sequence: SGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGKESKTPGKSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGSQEPMATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.943
R work: 0.1794
R free: 0.2227
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MOPS/HEPES-Na pH 7.5, 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.03 M sodium iodide
Matthews coefficient: 2.44
Solvent content (%): 49.53
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: 2019-11-13
KDR in complex with ligand sorafenib (PDB entry 3WZE)
Macromolecule: Vascular endothelial growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: DEHCERLPYDASKWEFPRDRLKLGKPLGRGAFGQVIEADAFGIDKTATCRTVAVKMLKEGATHSEHRALMSELKILIHIGHHLNVVNLLGACTKPGGPLMVIVEFCKFGNLSTYLRSKRNEFVPYKVAPEDLYKDFLTLEHLICYSFQVAKGMEFLASRKCIHRDLAARNILLSEKNVVKICDFGLARDIYKDPDYVRKGDARLPLKWMAPETIFDRVYTIQSDVWSFGVLLWEIFSLGASPYPGVKIDEEFCRRLKEGTRMRAPDYTTPEMYQTMLDCWHGEPSQRPTFSELVEHLGNLLQANAQQDG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.18479
R free: 0.22406
Average B factor: 48.93
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 10-25% PEG 3350, Na3Citrate, 0.1M Bis-Tris propane, pH 8.0, VAPOR DIFFUSION, temperature 277K
Matthews coefficient: 2.97
Solvent content (%): 58.68
Ligand: 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE (BAX)
Ligand formula: C21 H16 Cl F3 N4 O3
Ligand molecular weight: 464.825
Ligand SMILES: CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl
Ligand InChI: InChI=1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)
Release date: 2015-05-27
X-ray structure of MHV PLP2 (Cys1716Ser) catalytic mutant in complex with free ubiquitin (PDB entry 5WFI)
Macromolecule: papain-like protease
Type: Protein, polypeptide(L)
Source organism: Murine hepatitis virus strain A59
EC number: 3.4.22
Sequence length: 303 residues
Sequence: NKVDVLCTVDGVNFRSCCVAEGEVFGKTLGSVFCDGINVTKVRCSAIYKGKVFFQYSDLSEADLVAVKDAFGFDEPQLLKYYTMLGMCKWPVVVCGNYFAFKQSNNNSYINVACLMLQHLSLKFPKWQWQEAWNEFRSGKPLRFVSLVLAKGSFKFNEPSDSIDFMRVVLREADLSGATCNLEFVCKCGVKQEQRKGVDAVMHFGTLDKGDLVRGYNIACTCGSKLVHCTQFNVPFLICSNTPEGRKLPDDVVAANIFTGGSVGHYTHVKCKPKYQLYDACNVNKVSEAKGNFTDCLYLKNLK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.851
R work: 0.1571
R free: 0.1973
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 50 mM Tris, pH 7.5, 100 mM sodium chloride, 5 mM DTT, 0.2 M potassium formate, 20% PEG3350
Matthews coefficient: 2.55
Solvent content (%): 51.71
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: 2018-08-01