satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of the human METTL3-METTL14 complex with compound T30 (UZH1a) (PDB entry 7ACD)
Macromolecule: N6-adenosine-methyltransferase catalytic subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.348
Sequence length: 246 residues
Sequence: MGHHHHHHSSGRENLYFQGALTQSVGGDSSADRLFPPQWICCDIRYLDVSILGKFAVVMADPPWDIHMELPYGTLTDDEMRRLNIPVLQDDGFLFLWVTGRAMELGRECLNLWGYERVDEIIWVKTNQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNQGLDCDVIVAEVRSTSHKPDEIYGMIERLSPGTRKIELFGRPHNVQPNWITLGNQLDGIHLLDPDVVARFKQRYPDGIISKPKNL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1874
R free: 0.2317
Average B factor: 44.88
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350, 400mM Mg acetate
Matthews coefficient: 2.14
Solvent content (%): 42.51
Ligand: 4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-oxidanyl-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide (R72)
Ligand formula: C32 H42 N6 O3
Ligand molecular weight: 558.714
Ligand SMILES: CC1(CCN(CC1)Cc2ccc(c(c2)O)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NCc5ccccc5)O)C
Ligand InChI: InChI=1S/C32H42N6O3/c1-31(2)12-15-37(16-13-31)20-25-9-10-26(27(39)17-25)30(40)34-21-32(41)11-6-14-38(22-32)29-18-28(35-23-36-29)33-19-24-7-4-3-5-8-24/h3-5,7-10,17-18,23,39,41H,6,11-16,19-22H2,1-2H3,(H,34,40)(H,33,35,36)/t32-/m1/s1
Release date: 2020-10-28
O-GlcNAc Transferase in complex with covalent inhibitor (PDB entry 6E37)
Macromolecule: O-GlcNAc transferase subunit p110
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.1.255
Sequence length: 723 residues
Sequence: GPGSCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDFKSNGHIYDNRIVLNGIDLKAFLDSLPDVKIVKMKCPDGGDNADSSNTALNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIKPVE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.531
R work: 0.1671
R free: 0.2112
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 1.45 M potassium phosphate dibasic
10 mM EDTA
1% xylitol
Matthews coefficient: 3.15
Solvent content (%): 60.98
Ligand: (2S,3R,4R,5S,6R)-3-[(2E)-but-2-enoylamino]-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name) (HQV)
Ligand formula: C19 H29 N3 O16 P2 S
Ligand molecular weight: 649.457
Ligand SMILES: CC=CC(=O)NC1C(C(C(SC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O
Ligand InChI: InChI=1S/C19H29N3O16P2S/c1-2-3-10(24)20-12-15(28)14(27)9(6-23)41-18(12)37-40(33,34)38-39(31,32)35-7-8-13(26)16(29)17(36-8)22-5-4-11(25)21-19(22)30/h2-5,8-9,12-18,23,26-29H,6-7H2,1H3,(H,20,24)(H,31,32)(H,33,34)(H,21,25,30)/b3-2+/t8-,9-,12-,13-,14-,15-,16-,17-,18+/m1/s1
Release date: 2019-11-06
Crystal structure of Ribonucleotide reductase R1 subunit, RRM1 in complex with 5-chloro-N-((1S,2R)-2-(6-fluoro-2,3-dimethylphenyl)-1-(5-oxo-4,5-dihydro-1,3,4-oxadiazol-2-yl)propyl)-4-methyl-3,4-dihydro-2H-benzo[b][1,4]oxazine-8-sulfonamide (PDB entry 6LKM)
Macromolecule: Ribonucleoside-diphosphate reductase large subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.17.4.1
Sequence length: 669 residues
Sequence: GAILAARIAVSNLHKETKKVFSDVMEDLYNYINPHNGKHSPMVAKSTLDIVLANKDRLNSAIIYDRDFSYNYFGFKTLERSYLLKINGKVAERPQHMLMRVSVGIHKEDIDAAIETYNLLSERWFTHASPTLFNAGTNRPQLSSCFLLSMKDDSIEGIYDTLKQCALISKSAGGIGVAVSCIRATGSYIAGTNGNSNGLVPMLRVYNNTARYVDQGGNKRPGAFAIYLEPWHLDIFEFLDLKKNTGKEEQRARDLFFALWIPDLFMKRVETNQDWSLMCPNECPGLDEVWGEEFEKLYASYEKQGRVRKVVKAQQLWYAIIESQTETGTPYMLYKDSCNRKSNQQNLGTIKCSNLCTEIVEYTSKDEVAVCNLASLALNMYVTSEHTYDFKKLAEVTKVVVRNLNKIIDINYYPVPEACLSNKRHRPIGIGVQGLADAFILMRYPFESAEAQLLNKQIFETIYYGALEASCDLAKEQGPYETYEGSPVSKGILQYDMWNVTPTDLWDWKVLKEKIAKYGIRNSLLIAPMPTASTAQILGNNESIEPYTSNIYTRRVLSGEFQIVNPHLLKDLTERGLWHEEMKNQIIACNGSIQSIPEIPDDLKQLYKTVWEISQKTVLKMAAERGAFIDQSQSLNIHIAEPNYGKLTSMHFYGWKQGLKTGMYYLRTR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.2102
R free: 0.2771
Average B factor: 51.036
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 300
Crystal growth procedure: Sodium acetate buffer, PEG3350, Lithium sulfate
Matthews coefficient: 2.68
Solvent content (%): 54.07
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: 2020-12-23
Crystal Structure of UbcH5B in Complex with the RING-U5BR Fragment of AO7 (PDB entry 5D1K)
Macromolecule: Ubiquitin-conjugating enzyme E2 D2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2.19
Sequence length: 147 residues
Sequence: MALKRIHKELNDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1696
R free: 0.202
Average B factor: 29.4482
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: 20% PEG-10000, 8% ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Matthews coefficient: 2.23
Solvent content (%): 44.86
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: 2015-10-28
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z927400026 (PDB entry 5RYB)
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): 1.55
R work: 0.1841
R free: 0.2158
Average B factor: 17.74
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: 2.08
Solvent content (%): 40.84
Ligand: (2S)-2-amino-3-methyl-1-(morpholin-4-yl)butan-1-one (WKM)
Ligand formula: C9 H18 N2 O2
Ligand molecular weight: 186.251
Ligand SMILES: CC(C)C(C(=O)N1CCOCC1)N
Ligand InChI: InChI=1S/C9H18N2O2/c1-7(2)8(10)9(12)11-3-5-13-6-4-11/h7-8H,3-6,10H2,1-2H3/t8-/m0/s1
Release date: 2020-11-11
Crystal structure of c-MET bound by compound 6 (PDB entry 7B40)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: GNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.76
R work: 0.196
R free: 0.232
Average B factor: 36.83
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20 % PEG4000, 10 % isopropanol, 0.1 M Na-HEPES pH 7.5
Matthews coefficient: 2.55
Solvent content (%): 51.78
Ligand: 3-(phenylmethyl)-5-(1-piperidin-4-ylpyrazol-4-yl)-1~{H}-pyrrolo[2,3-b]pyridine (SWN)
Ligand formula: C22 H23 N5
Ligand molecular weight: 357.452
Ligand SMILES: c1ccc(cc1)Cc2c[nH]c3c2cc(cn3)c4cnn(c4)C5CCNCC5
Ligand InChI: InChI=1S/C22H23N5/c1-2-4-16(5-3-1)10-18-13-25-22-21(18)11-17(12-24-22)19-14-26-27(15-19)20-6-8-23-9-7-20/h1-5,11-15,20,23H,6-10H2,(H,24,25)
Release date: 2020-12-09
Crystal structure of the C. elegans Protein O-fucosyltransferase 2 (CePOFUT2) double mutant (R298K-R299K) in complex with GDP and the human TSR1 from thrombospondin 1 (PDB entry 5FOE)
Macromolecule: GDP-fucose protein O-fucosyltransferase 2,Thrombospondin-1
Type: Protein, polypeptide(L)
Source organism: Caenorhabditis elegans
EC number: 2.4.1.221
Sequence length: 500 residues
Sequence: MHFFPIQLLVLFFAEKIAFAENSDQTVSRVDSNRYSVAAEKKFLLYDVNFGEGFNLRRDVYMRVANTVRSLRDSGENYILVLPPWGRLHHWKRMEVALSWRLFFDLESLNRFIPVIEFEDFLDENRPIDQVIYLQHYAEGWGTEYVRKFEKRSCLPPAESHYKQVEEFKWKGWFYSYEDVYSRNFQCVSIQGDSGTLKDLLKHSNFSESTSIMVDRAETILHEHYGEVDYWKARRSMRYSNDLVDVADAFRKKYLDSDDKRDKTKLVDDWTKEKPRRTAIGGPYLGIHWRRRDFLYAKKAQLPTIPGTAKILQDLCKKLDLQKIYLATDAPDQEVDELKALLNGELEVYRFTDTQKLNDGQIAIIDQYLCAHAAYFIGSYESTFTFRIQEDREIIGFPISTTFNRLCPDTEPTCEQPAKWKIVYSSSSGGGGSGGGGSGGGGGSSGSSADDGWSPWSEWTSCSTSCGNGIQQRGRSCDSLNNRCEGSSVQTRTCHIQECD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.20044
R free: 0.24607
Average B factor: 35.795
Matthews coefficient: 2.15
Solvent content (%): 42.82
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: 2016-01-27
CDK2 in complex with FragLite38 (PDB entry 6Q4K)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 306 residues
Sequence: GPLGSPEFMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.06
R work: 0.14312
R free: 0.16216
Average B factor: 19.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 10MG/ML CDK2 10% V/V PEG3350, 50 MM HEPES/NAOH, 50 MM NA/K PHOSPHATE, PH 7.5
Matthews coefficient: 1.95
Solvent content (%): 37.04
Ligand: (~{E})-3-[3-[(4-chlorophenyl)carbamoyl]phenyl]prop-2-enoic acid (HHW)
Ligand formula: C16 H12 Cl N O3
Ligand molecular weight: 301.724
Ligand SMILES: c1cc(cc(c1)C(=O)Nc2ccc(cc2)Cl)C=CC(=O)O
Ligand InChI: InChI=1S/C16H12ClNO3/c17-13-5-7-14(8-6-13)18-16(21)12-3-1-2-11(10-12)4-9-15(19)20/h1-10H,(H,18,21)(H,19,20)/b9-4+
Release date: 2019-03-20
Design, Synthesis, and Evaluation of the First Selective and Potent G-protein-Coupled Receptor Kinase 2 (GRK2) Inhibitor for the Potential Treatment of Heart Failure (PDB entry 5UVC)
Macromolecule: Beta-adrenergic receptor kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.15
Sequence length: 547 residues
Sequence: MSYYHHHHHHDYDIPTTENLYFQGAMEPGGSTPAARASKKILLPEPSIRSVMQKYLEDRGEVTFEKIFSQKLGYLLFRDFCLNHLEEARPLVEFYEEIKKYEKLETEEERVARSREIFDSYIMKELLACSHPFSKSATEHVQGHLGKKQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFCQWKNVELNIHLTMNDFSVHRIIGRGGFGEVYGCRKADTGKMYAMKCLDKKRIKMKQGETLALNERIMLSLVSTGDCPFIVCMSYAFHTPDKLSFILDLMNGGDLHYHLSQHGVFSEADMRFYAAEIILGLEHMHNRFVVYRDLKPANILLDEHGHVRISDLGLACDFSKKKPHASVGTHGYMAPEVLQKGVAYDSSADWFSLGCMLFKLLRGHSPFRQHKTKDKHEIDRMTLTMAVELPDSFSPELRSLLEGLLQRDVNRRLGCLGRGAQEVKESPFFRSLDWQMVFLQKYPPPLIPPRGEVNAADAFDIGSFDEEDTKGIKLLDSDQELYRNFPLTISERWQQEVAETVFDTINAETDRLEA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.2145
R free: 0.2603
Average B factor: 60.002
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.9
Crystallization temperature (K): 273
Crystal growth procedure: 18% PEG MME 2000, 100mM MES pH 5.9, 17.5mM Ammonium Sulfate
Matthews coefficient: 2.42
Solvent content (%): 49.08
Ligand: N-benzyl-3-({[5-(pyridin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)benzamide (8PV)
Ligand formula: C22 H20 N6 O
Ligand molecular weight: 384.434
Ligand SMILES: c1ccc(cc1)CNC(=O)c2cccc(c2)NCc3[nH]c(nn3)c4ccncc4
Ligand InChI: InChI=1S/C22H20N6O/c29-22(25-14-16-5-2-1-3-6-16)18-7-4-8-19(13-18)24-15-20-26-21(28-27-20)17-9-11-23-12-10-17/h1-13,24H,14-15H2,(H,25,29)(H,26,27,28)
Release date: 2017-07-26
HsMetAP complex with (1-amino-2-methylpentyl)phosphonic acid (PDB entry 4U69)
Macromolecule: Methionine aminopeptidase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 306 residues
Sequence: YRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKLLSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCYPSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHGDLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHAQANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMICEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARPHFMSQF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.17
R free: 0.202
Average B factor: 24.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: PEG 2000, potassium chloride, hepes, sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Matthews coefficient: 2.57
Solvent content (%): 52.08
Ligand: POTASSIUM ION (K)
Ligand formula: K
Ligand molecular weight: 39.098
Ligand SMILES: [K+]
Ligand InChI: InChI=1S/K/q+1
Release date: 2015-03-25
Structure of cyclophilin A in complex with 3,4-diaminobenzohydrazide (PDB entry 5NOZ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 165 residues
Sequence: MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.18834
R free: 0.21609
Average B factor: 21.286
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 279.15
Crystal growth procedure: PEG 8000, Tris-HCl
Matthews coefficient: 2.8
Solvent content (%): 56.06
Ligand: 3,4-bis(azanyl)benzohydrazide (L99)
Ligand formula: C7 H10 N4 O
Ligand molecular weight: 166.18
Ligand SMILES: c1cc(c(cc1C(=O)NN)N)N
Ligand InChI: InChI=1S/C7H10N4O/c8-5-2-1-4(3-6(5)9)7(12)11-10/h1-3H,8-10H2,(H,11,12)
Release date: 2017-07-12
CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH 5-[3-[(3-chloro-8-quinolyl)amino]phenyl]-5-methyl-2,6-dihydro-1,4-oxazin-3-amine (PDB entry 5F00)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 390 residues
Sequence: RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVASIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.22033
R free: 0.26344
Average B factor: 30.896
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: 2.5M SODIUM FORMATE, 100MM HEPES
Matthews coefficient: 3.15
Solvent content (%): 61.01
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2016-02-24
LINKED KDM5A JMJ DOMAIN BOUND TO THE POTENTIAL HYDROLYSIS PRODUCT OF INHIBITOR N45 i.e. 3-((6-(4-(2-cyano-3-methylbut-2-enoyl)-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid (PDB entry 6DQ7)
Macromolecule: Linked KDM5A Jmj Domain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 330 residues
Sequence: HNMAGVGPGGYAAEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPFACEVKSFRFTPRVQRLNELEAMTRVRPREAFGFEQAVREYTLQSFGEMADNFKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.852
R work: 0.1918
R free: 0.2093
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 289
Crystal growth procedure: 1.2-1.35 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.6-9.2) 0-20% glycerol 25 mM (Na/K) dibasic/monobasic phosphate
Matthews coefficient: 2.25
Solvent content (%): 45.35
Ligand: N-{6-[4-(hydroxyacetyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine (H6M)
Ligand formula: C19 H24 N6 O4
Ligand molecular weight: 400.432
Ligand SMILES: c1ccnc(c1)c2nc(cc(n2)N3CCCN(CC3)C(=O)CO)NCCC(=O)O
Ligand InChI: InChI=1S/C19H24N6O4/c26-13-17(27)25-9-3-8-24(10-11-25)16-12-15(21-7-5-18(28)29)22-19(23-16)14-4-1-2-6-20-14/h1-2,4,6,12,26H,3,5,7-11,13H2,(H,28,29)(H,21,22,23)
Release date: 2019-06-12
JNK3 (Mitogen-activated protein kinase 10) in Complex with Compound 23 bearing a C(sp3)F2Br moiety (PDB entry 8BZP)
Macromolecule: Mitogen-activated protein kinase 10
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 364 residues
Sequence: MSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.1894
R free: 0.2162
Average B factor: 46.16
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: Protein was concentrated to 7-9 mg/ml and incubated with (final conc.): 1mM AMP-PCP, 0.4 mM Zwittergent and 10% EG. Protein was mixed 2+2 ul with mother liquor containing: 100 mM BisTris pH=6, PEG3350 27% and NaCl 200 mM
Matthews coefficient: 2.23
Solvent content (%): 44.81
Ligand: 2-bromanyl-2,2-bis(fluoranyl)-~{N}-(5-pyridin-4-yl-1,3,4-thiadiazol-2-yl)ethanamide (SWM)
Ligand formula: C9 H5 Br F2 N4 O S
Ligand molecular weight: 335.128
Ligand SMILES: c1cnccc1c2nnc(s2)NC(=O)C(F)(F)Br
Ligand InChI: InChI=1S/C9H5BrF2N4OS/c10-9(11,12)7(17)14-8-16-15-6(18-8)5-1-3-13-4-2-5/h1-4H,(H,14,16,17)
Release date: 2023-08-02
Crystal structure of the TIR domain of human TLR1 (crystallised without ZN2+ ions) (PDB entry 7NUX)
Macromolecule: Toll-like receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2.6
Sequence length: 162 residues
Sequence: SNIPLEELQRNLQFHAFISYSGHDSFWVKNELLPNLEKEGMQICLHERNFVPGKSIVENIITCIEKSYKSIFVLSPNFVQSEWCHYELYFAHHNLFHEGSNSLILILLEPIPQYSIPSSYHKLKSLMARRTYLEWPKEKSKRGLFWANLRAAINIKLTEQAK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.47
R work: 0.2292
R free: 0.2788
Average B factor: 55.61
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.6
Crystallization temperature (K): 277
Crystal growth procedure: 170 mM Ammonium acetate, 85 mM Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4,000, 15% v/v glycerol (#9 from HR2-122 Hampton)
Growth at +4 for 3-4 months.
Matthews coefficient: 2.67
Solvent content (%): 53.95
Release date: 2021-08-25
The Crystal Structure of CDK3 and CyclinE1 Complex with Dinaciclib from Biortus (PDB entry 8H4R)
Macromolecule: Glutathione S-transferase class-mu 26 kDa isozyme,Cyclin-dependent kinase 3
Type: Protein, polypeptide(L)
Source organism: Schistosoma japonicum
EC number: 2.5.1.18
Sequence length: 533 residues
Sequence: MSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAYSKDFETLKVDFLSKLPEMLKMFEDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLDAFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDLEVLFQGPMDMFQKVEKIGEGTYGVVYKAKNRETGQLVALKKIRLDLEMEGVPSTAIREISLLKELKHPNIVRLLDVVHNERKLYLVFEFLSQDLKKYMDSTPGSELPLHLIKSYLFQLLQGVSFCHSHRVIHRDLKPQNLLINELGAIKLADFGLARAFGVPLRTYTHEVVTLWYRAPEILLGSKFYTTAVDIWSIGCIFAEMVTRKALFPGDSEIDQLFRIFRMLGTPSEDTWPGVTQLPDYKGSFPKWTRKGLEEIVPNLEPEGRDLLMQLLQYDPSQRITAKTALAHPYFSSPEPSPAARQYVLQRFRH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.1614
R free: 0.2234
Average B factor: 35.299
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.6M MgSO4, 0.1M MES pH 6.60
Matthews coefficient: 2.73
Solvent content (%): 54.93
Ligand: 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium (1QK)
Ligand formula: C21 H29 N6 O2
Ligand molecular weight: 397.494
Ligand SMILES: CCc1cnn2c1nc(cc2NCc3ccc[n+](c3)O)N4CCCCC4CCO
Ligand InChI: InChI=1S/C21H29N6O2/c1-2-17-14-23-27-19(22-13-16-6-5-9-25(29)15-16)12-20(24-21(17)27)26-10-4-3-7-18(26)8-11-28/h5-6,9,12,14-15,18,22,28-29H,2-4,7-8,10-11,13H2,1H3/q+1/t18-/m0/s1
Release date: 2023-10-11
The crystal structure of human MACROD2 in space group P41212 (PDB entry 6Y4Y)
Macromolecule: Thioredoxin 1,ADP-ribose glycohydrolase MACROD2
Type: Protein, polypeptide(L)
Source organism: Escherichia coli K-12
EC number: 3.5.1
Sequence length: 366 residues
Sequence: MHHHHHHSSGMSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAGTENLYFQSMKKKVWREEKERLLKMTLEERRKEYLRDYIPLNSILSWKEEMKGKGQNDEENTQETSQVKKSLTEKVSLYRGDITLLEVDAIVNAANASLLGGGGVDGCIHRAAGPCLLAECRNLNGCDTGHAKITCGYDLPAKYVIHTVGPIARGHINGSHKEDLANCYKSSLKLVKENNIRSVAFPCISTGIYGFPNEPAAVIALNTIKEWLAKNHHEVDRIIFCVFLEVDFKIYKKKMNEFFSVD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.2043
R free: 0.2274
Average B factor: 33.887
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.7
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350
Ligand: L(+)-TARTARIC ACID (TLA)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m1/s1
Release date: 2020-09-30