satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of TNKS2 in complex with 2-(4-((pyridin-4-yl)methyl) piperazin-1-yl)-3,4,5,6,7,8-hexahydroquinazolin-4-one (PDB entry 5AL5)
Macromolecule: TANKYRASE-2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 240 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMLNTSGSGTILIDLSPDDKEFQSVEEEMQSTVREHRDGGHAGGIFNRYNILKIQKVCNKKLWERYTHRRKEVSEENHNHANERMLFHGSPFVNAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPVHKDRSCYICHRQLLFCRVTLGKSFLQFSAMKMAHSPPGHHSVTGRPSVNGLALAEYVIYRGEQAYPEYLITYQIMRPEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.05
R work: 0.17372
R free: 0.22253
Average B factor: 29.689
Crystallization pH: 8.5
Crystal growth procedure: pH 8.5
Matthews coefficient: 2.4
Solvent content (%): 49
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: 2015-07-29
ATAD2 in complex with PepLite-Arg (PDB entry 7Z9S)
Macromolecule: ATPase family AAA domain-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.3
Sequence length: 130 residues
Sequence: SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICSNALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.2039
R free: 0.2362
Average B factor: 35.981
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M BisTris pH 6-7, 1.7-2.1M Ammonium sulphate
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: 2022-11-23
Lysosomal Phospholipase A2 in complex with Zinc (PDB entry 6MTW)
Macromolecule: Group XV phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1
Sequence length: 380 residues
Sequence: GAGRHPPVVLVPGDLGNQLEAKLDKPTVVHYLCSKKTESYFTIWLNLELLLPVIIDCWIDNIRLVYNKTSRATQFPDGVDVRVPGFGKTFSLEFLDPSKSSVGSYFHTMVESLVGWGYTRGEDVRGAPYDWRRAPNENGPYFLALREMIEEMYQLYGGPVVLVAHSMGNMYTLYFLQRQPQAWKDKYIRAFVSLGAPWGGVAKTLRVLASGDNNRIPVIGPLKIREQQRSAVSTSWLLPYNYTWSPEKVFVQTPTINYTLRDYRKFFQDIGFEDGWLMRQDTEGLVEATMPPGVQLHCLYGTGVPTPDSFYYESFPDRDPKICFGDGDGTVNLKSALQCQAWQSRQEHQVLLQELPGSEHIEMLANATTLAYLKRVLLGP
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.999
R work: 0.2475
R free: 0.2848
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium cacodylate pH 5.6, 6% isopropanol, 250 mM zinc acetate, 2 mM 1-hydroxy-2-azelaoyl-sn-glycero-3-phosphocholine
Matthews coefficient: 2.57
Solvent content (%): 52.09
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2019-03-20
IDO1/FXB-001116 crystal structure (PDB entry 6AZW)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 394 residues
Sequence: MISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.78
R work: 0.2166
R free: 0.2986
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: 16% PEG 8K, 0.2 M NH4 acetate, 0.1 M CHES pH 8.75
Matthews coefficient: 2.86
Solvent content (%): 57
Ligand: (2R)-N-(4-cyanophenyl)-2-[cis-4-(quinolin-4-yl)cyclohexyl]propanamide (C51)
Ligand formula: C25 H25 N3 O
Ligand molecular weight: 383.486
Ligand SMILES: CC(C1CCC(CC1)c2ccnc3c2cccc3)C(=O)Nc4ccc(cc4)C#N
Ligand InChI: InChI=1S/C25H25N3O/c1-17(25(29)28-21-12-6-18(16-26)7-13-21)19-8-10-20(11-9-19)22-14-15-27-24-5-3-2-4-23(22)24/h2-7,12-15,17,19-20H,8-11H2,1H3,(H,28,29)/t17-,19-,20+/m1/s1
Release date: 2018-03-21
Structure of UbE2D2:RNF165:Ub complex (PDB entry 5D0K)
Macromolecule: Ubiquitin-conjugating enzyme E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2.19
Sequence length: 152 residues
Sequence: GPLGSMALKRIHKELNDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.1919
R free: 0.2377
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: MES, sodium chloride, PEG 6000
Matthews coefficient: 3.62
Solvent content (%): 66.01
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: 2015-12-09
Crystal structure of JAK3 in complex with peficitinib (PDB entry 6AAK)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 287 residues
Sequence: PTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.67
R work: 0.269
R free: 0.326
Average B factor: 39.51
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: buffer, salt, precipitant
Matthews coefficient: 2.72
Solvent content (%): 54.87
Ligand: 4-[[(1S,3R)-5-oxidanyl-2-adamantyl]amino]-1H-pyrrolo[2,3-b]pyridine-5-carboxamide (9T6)
Ligand formula: C18 H22 N4 O2
Ligand molecular weight: 326.393
Ligand SMILES: c1c[nH]c2c1c(c(cn2)C(=O)N)NC3C4CC5CC3CC(C5)(C4)O
Ligand InChI: InChI=1S/C18H22N4O2/c19-16(23)13-8-21-17-12(1-2-20-17)15(13)22-14-10-3-9-4-11(14)7-18(24,5-9)6-10/h1-2,8-11,14,24H,3-7H2,(H2,19,23)(H2,20,21,22)/t9-,10-,11+,14-,18-
Release date: 2018-08-15
Crystal structure of Angiotensin-1 converting enzyme C-domain in complex with dual ACE/NEP inhibitor AD013 (PDB entry 7Q29)
Macromolecule: Angiotensin-converting enzyme
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1
Sequence length: 597 residues
Sequence: LVTDEAEASKFVEEYDRTSQVVWNEYAGANWNYNTNITTETSKILLQKNMQIAQHTLKYGTQARKFDVNQLQNTTIKRIIKKVQDLERAALPAQELEEYNKILLDMETTYSVATVCHPQGSCLQLEPDLTNVMATSRKYEDLLWAWEGWRDKAGRAILQFYPKYVELINQAARLNGYVDAGDSWRSMYETPSLEQDLERLFQELQPLYLNLHAYVRRALHRHYGAQHINLEGPIPAHLLGNMWAQTWSNIYDLVVPFPSAPSMDTTEAMLKQGWTPRRMFKEADDFFTSLGLLPVPPEFWQKSMLEKPTDGREVVCHASAWDFYNGKDFRIKQCTTVNLEDLVVAHHEMGHIQYFMQYKDLPVALREGANPGFHEAIGDVLALSVSTPKHLHSLNLLSSEGGSDEHDINFLMKMALDKIAFIPFSYLVDQWRWRVFDGSITKENYNQEWWSLRLKYQGLCPPVPRTQGDFDPGAKFHIPSSVPYIRYFVSFIIQFQFHEALCQAAGHTGPLHKCDIYQSKEAGQRLATAMKLGFSRPWPEAMQLITGQPQMSASAMLSYFKPLLDWLRTENELHGEKLGWPQYNWTPNSARSEGPLP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1605
R free: 0.1843
Average B factor: 21.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4
Crystallization temperature (K): 289
Crystal growth procedure: 0.1 M MIB pH 4.0, 5% glycerol, 15% PEG 3350
Matthews coefficient: 2.29
Solvent content (%): 46.38
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2022-02-16
Human DNA polymerase beta crosslinked binary complex - B (PDB entry 7RBF)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACGGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.84
R work: 0.1759
R free: 0.2083
Average B factor: 26.104
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M Citrate pH 5.5, 18% PEG6000
Matthews coefficient: 2.46
Solvent content (%): 49.91
Ligand: 2-deoxy-3,5-di-O-phosphono-D-erythro-pentitol (QPJ)
Ligand formula: C5 H14 O10 P2
Ligand molecular weight: 296.106
Ligand SMILES: C(CO)C(C(COP(=O)(O)O)O)OP(=O)(O)O
Ligand InChI: InChI=1S/C5H14O10P2/c6-2-1-5(15-17(11,12)13)4(7)3-14-16(8,9)10/h4-7H,1-3H2,(H2,8,9,10)(H2,11,12,13)/t4-,5+/m1/s1
Release date: 2022-03-09
Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 3 (PDB entry 8OG8)
Macromolecule: DDB1- and CUL4-associated factor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 367 residues
Sequence: GGGREPKQRRQAPINFTSRLNRRASFPKYGGVDGGCFDRHLIFSRFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSALAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVGRQRLAEDEDEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.1736
R free: 0.2125
Average B factor: 30.084
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MES pH6.5, 2.13M Lithium acetate
Matthews coefficient: 2.69
Solvent content (%): 54.35
Ligand: 5-(2-methyl-1-phenyl-propan-2-yl)imidazo[2,1-a]isoquinoline (VM8)
Ligand formula: C21 H20 N2
Ligand molecular weight: 300.397
Ligand SMILES: CC(C)(Cc1ccccc1)c2cc3ccccc3c4n2ccn4
Ligand InChI: InChI=1S/C21H20N2/c1-21(2,15-16-8-4-3-5-9-16)19-14-17-10-6-7-11-18(17)20-22-12-13-23(19)20/h3-14H,15H2,1-2H3
Release date: 2023-06-14
JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3 (13-mer) (PDB entry 5LY2)
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: Hetero 8-mer
Stoichiometry: A4, B2, C2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.43
R work: 0.219
R free: 0.245
Average B factor: 43
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M bicine pH 9.0 and 10% w/v polyethylene glycol 6000
Matthews coefficient: 2.3
Solvent content (%): 46.47
Ligand: NICKEL (II) ION (NI)
Ligand formula: Ni
Ligand molecular weight: 58.693
Ligand SMILES: [Ni+2]
Ligand InChI: InChI=1S/Ni/q+2
Release date: 2017-04-12
Crystal structure of wild-type c-MET bound by compound 7. (PDB entry 8AN8)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 296 residues
Sequence: GHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.394
R work: 0.2411
R free: 0.298
Average B factor: 41.24
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.4 M am sulfate, PCPT pH 5.5
Matthews coefficient: 2.52
Solvent content (%): 51.27
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: 2022-08-31
PHF2 PHD Domain Complexed with Peptide From N-terminus of VRK1 (PDB entry 7M10)
Macromolecule: Lysine-specific demethylase PHF2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 74 residues
Sequence: GSINMATVPVYCVCRLPYDVTRFMIECDACKDWFHGSCVGVEEEEAPDIDIYHCPNCEKTHGKSTLKKKRTWHK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.15
R work: 0.1565
R free: 0.1648
Average B factor: 20.61
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.2
Crystallization temperature (K): 292
Crystal growth procedure: 3.5M Sodium Formate,100mM TRIS pH 8.2
Matthews coefficient: 2.86
Solvent content (%): 56.93
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2021-05-26
FACTOR XIA (PICHIA PASTORIS; C500S [C122S]) IN COMPLEX WITH THE INHIBITOR (2E)-N-{(1S)-1-[4-(3-amino-1H-indazol-6-yl)-1H-imidazol-2-yl]-2-phenylethyl}-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enamide (PDB entry 4X6P)
Macromolecule: Coagulation factor XI, light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 238 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVNYTDSQRPISLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.164
R free: 0.1965
Average B factor: 24.3
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 277
Crystal growth procedure: 100 MM SODIUM CITRATE, PH 5.0, 36%(w/v) PEG4000
Matthews coefficient: 2.31
Solvent content (%): 46.8
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2015-02-18
Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5-(PA)2-IP4 (PDB entry 5BYB)
Macromolecule: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.4.21
Sequence length: 330 residues
Sequence: GSFTERQIVVGICSMAKKSKSKPMKEILERISLFKYITVVVFEEEVILNEPVENWPLCDCLISFHSKGFPLDKAVAYAKLRNPFVINDLNMQYLIQDRREVYSILQAEGILLPRYAILNRDPNNPKECNLIEGEDHVEVNGEVFQKPFVEKPVSAEDHNVYIYYPTSAGGGSQRLFRKIGSRSSVYSPESNVRKTGSYIYEEFMPTDGTDVKVYTVGPDYAHAEARKSPALDGKVERDSEGKEVRYPVILNAREKLIAWKVCLAFKQTVCGFDLLRANGQSYVCDVNGFSFVKNSMKYYDDCAKILGNIVMRELAPQFHIPWSIPLEAED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.18935
R free: 0.24638
Average B factor: 22.434
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 277
Crystal growth procedure: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM ATP and 2 mM CdCl2. The crystals were transferred to a stabilizing buffer containing 22% (w/v) PEG 3350, 10 mM MgCl2, 0.1 M sodium acetate, pH 5.2 at 4 oC overnight, while ATP in the crystals was hydrolyzed to ADP. The crystals were soaked under the above stabilizing buffer for three days with 2 mM analog.
Matthews coefficient: 2.81
Solvent content (%): 56.24
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: 2015-07-22
Crystal Structure of human ETB receptor in complex with Endothelin-3 (PDB entry 6IGK)
Macromolecule: Endothelin receptor type B,Endolysin,Endothelin receptor type B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.17
Sequence length: 498 residues
Sequence: GGGLAPAEVPKGDRTAGSPPRTISPPPCQGPIEIKETFKYINTVVSCLVFVLGIIGNSTLLYIIYKNKCMRNGPNILIASLALGDLLHIVIAIPINVYKLLAEDWPFGAEMCKLVPFIQKASVGITVLSLCALSIDRYRAVASWSRIKGIGVPKWTAVEIVLIWVVSVVLAVPEAIGFDIITMDYKGSYLRICLLHPVQKTAFMQFYATAKDWWLFSFYFCLPLAITAFFYTLMTCEMLRKNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYLNDHLKQRREVAKTVFCLVLVFALCWLPLHLARILKLTLYNQNDPNRCELLSFLLVLDYIGINMASLNSCANPIALYLVSKRFKNAFKSALCCWAQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1834
R free: 0.2271
Average B factor: 47.0245
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: PEG 500DME, Ammonium citrate tribasic
Matthews coefficient: 2.92
Solvent content (%): 57.91
Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (OLC)
Ligand formula: C21 H40 O4
Ligand molecular weight: 356.54
Ligand SMILES: CCCCCCCCC=CCCCCCCCC(=O)OCC(CO)O
Ligand InChI: InChI=1S/C21H40O4/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-21(24)25-19-20(23)18-22/h9-10,20,22-23H,2-8,11-19H2,1H3/b10-9-/t20-/m1/s1
Release date: 2018-11-21
Crystal Structure of Factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-2-(3-chlorophenyl)acetamide (PDB entry 5PAT)
Macromolecule: Coagulation factor VII light chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 64 residues
Sequence: LICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKRNASKPQGR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1859
R free: 0.2166
Average B factor: 23.755
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol
Matthews coefficient: 3.75
Solvent content (%): 67.18
Ligand: N-(2-amino-1H-benzimidazol-5-yl)-2-(3-chlorophenyl)acetamide (7ZG)
Ligand formula: C15 H13 Cl N4 O
Ligand molecular weight: 300.743
Ligand SMILES: c1cc(cc(c1)Cl)CC(=O)Nc2ccc3c(c2)[nH]c(n3)N
Ligand InChI: InChI=1S/C15H13ClN4O/c16-10-3-1-2-9(6-10)7-14(21)18-11-4-5-12-13(8-11)20-15(17)19-12/h1-6,8H,7H2,(H,18,21)(H3,17,19,20)
Release date: 2017-06-21
Crystal Structure of KSR1:MEK1 in complex with AMP-PNP (PDB entry 7JUW)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 1
Type: Protein, polypeptide(L)
Source organism: Oryctolagus cuniculus
EC number: 2.7.12.2
Sequence length: 384 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEKISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGCQVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSAVFSLEFQDFVNKCLIKNPAERADLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.88
R work: 0.2432
R free: 0.2859
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 2000, MES pH 6.5, Magnesium Acetate
Matthews coefficient: 3.67
Solvent content (%): 72.43
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER (ANP)
Ligand formula: C10 H17 N6 O12 P3
Ligand molecular weight: 506.196
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
Release date: 2020-09-30
Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-226 (PDB entry 6FDI)
Macromolecule: cAMP-specific 3',5'-cyclic phosphodiesterase 4D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.53
Sequence length: 364 residues
Sequence: GSHMIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQSPSPAPDDPEEGRQGQTEKFQFELTL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.17357
R free: 0.19998
Average B factor: 31.576
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 24% PEG 3350, 30% Ethylene Glycol, 0.1 M HEPES
Matthews coefficient: 2.65
Solvent content (%): 53.54
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2019-04-10
Crystal structure of human histone deacetylase 8 (HDAC8) I45T mutation complexed with SAHA (PDB entry 7JVU)
Macromolecule: Histone deacetylase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 389 residues
Sequence: MEEPEEPADSGQSLVPVYIYSPEYVSMCDSLAKIPKRASMVHSLTEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVIEGRGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5004765401
R work: 0.164399381995
R free: 0.184587196948
Average B factor: 22.8636882906
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.1 M imidazole, pH 7.0, 15% PEG35000, 4 mM TCEP
Matthews coefficient: 2.42
Solvent content (%): 49.07
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: 2020-12-16