satarupa22/MacromolecularLigandDB huggingface dataset:
FACTOR VIIA IN COMPLEX WITH THE INHIBITOR (methyl {3-[(2R)-1-{(2R)-2-(3,4-dimethoxyphenyl)-2-[(1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]acetyl}pyrrolidin-2-yl]-4-(propan-2-ylsulfonyl)phenyl}carbamate) (PDB entry 4X8V)
Macromolecule: Factor VIIa (Light Chain)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.21
Sequence length: 55 residues
Sequence: ICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILEKR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1931
R free: 0.2297
Average B factor: 30.77
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000
Matthews coefficient: 3.87
Solvent content (%): 68.2
Ligand: methyl {3-[(2R)-1-{(2R)-2-(3,4-dimethoxyphenyl)-2-[(1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]acetyl}pyrrolidin-2-yl]-4-(propan-2-ylsulfonyl)phenyl}carbamate (3Z9)
Ligand formula: C34 H40 N4 O8 S
Ligand molecular weight: 664.768
Ligand SMILES: CC(C)S(=O)(=O)c1ccc(cc1C2CCCN2C(=O)C(c3ccc(c(c3)OC)OC)Nc4ccc5c(c4)C(=O)NCC5)NC(=O)OC
Ligand InChI: InChI=1S/C34H40N4O8S/c1-20(2)47(42,43)30-13-11-24(37-34(41)46-5)19-26(30)27-7-6-16-38(27)33(40)31(22-9-12-28(44-3)29(17-22)45-4)36-23-10-8-21-14-15-35-32(39)25(21)18-23/h8-13,17-20,27,31,36H,6-7,14-16H2,1-5H3,(H,35,39)(H,37,41)/t27-,31-/m1/s1
Release date: 2015-03-25
Structure of the complex of VPS4B MIT and IST1 MIM (PDB entry 4U7Y)
Macromolecule: Vacuolar protein sorting-associated protein 4B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.6
Sequence length: 90 residues
Sequence: SMSSTSPNLQKAIDLASKAAQEDKAGNYEEALQLYQHAVQYFLHVVKYEAQGDKAKQSIRAKCTEYLDRAEKLKEYLKNKEKKAQKPVKE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.502
R work: 0.2252
R free: 0.2713
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 299
Crystal growth procedure: 2.58 M Na-malonate
Matthews coefficient: 2.25
Solvent content (%): 45.4
Release date: 2015-02-11
Crystal Structure of human phosphodiesterase 10 in complex with 5,7,8-trimethyl-2-[2-(2-methyl-5-pyrrolidin-1-yl-1,2,4-triazol-3-yl)ethyl]-[1,2,4]triazolo[1,5-c]pyrimidine (PDB entry 5SEF)
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): 2.29
R work: 0.172
R free: 0.2323
Average B factor: 54.924
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 (%): 53.34
Ligand: (4R)-5,7,8-trimethyl-2-{2-[1-methyl-3-(pyrrolidin-1-yl)-1H-1,2,4-triazol-5-yl]ethyl}[1,2,4]triazolo[1,5-c]pyrimidine (IFR)
Ligand formula: C17 H24 N8
Ligand molecular weight: 340.426
Ligand SMILES: Cc1c(nc(n2c1nc(n2)CCc3nc(nn3C)N4CCCC4)C)C
Ligand InChI: InChI=1S/C17H24N8/c1-11-12(2)18-13(3)25-16(11)19-14(21-25)7-8-15-20-17(22-23(15)4)24-9-5-6-10-24/h5-10H2,1-4H3
Release date: 2022-10-12
Carbonic Anhydrase IX Mimic Complexed with N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)cyclohexanecarboxamide (PDB entry 7JOB)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.381
R work: 0.1702
R free: 0.191
Average B factor: 17.1064
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris
Matthews coefficient: 2.03
Solvent content (%): 39.55
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: 2020-11-04
Crystal structure of human pyridoxal 5'-phosphate phosphatase (Chronophin) mutant - C221S (PDB entry 5GYN)
Macromolecule: Pyridoxal phosphate phosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.3
Sequence length: 301 residues
Sequence: GAMDPMARCERLRGAALRDVLGRAQGVLFDCDGVLWNGERAVPGAPELLERLARAGKAALFVSNNSRRARPELALRFARLGFGGLRAEQLFSSALCAARLLRQRLPGPPDAPGAVFVLGGEGLRAELRAAGLRLAGDPSAGDGAAPRVRAVLVGYDEHFSFAKLREACAHLRDPECLLVATDRDPWHPLSDGSRTPGTGSLAAAVETASGRQALVVGKPSPYMFESITENFSIDPARTLMVGDRLETDILFGHRCGMTTVLTLTGVSRLEEAQAYLAAGQHDLVPHYYVESIADLTEGLED
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.995
R work: 0.196
R free: 0.2339
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 294
Crystal growth procedure: 16% PEG 4000, 20 mM magnesium chloride, 100 mM HEPES pH7.0
Matthews coefficient: 2.48
Solvent content (%): 50.42
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: 2017-09-27
Crystal structure of MORN4/Myo3a complex (PDB entry 6JLE)
Macromolecule: MORN repeat-containing protein 4
Type: Protein, polypeptide(L)
Source organism: Mus musculus
Sequence length: 146 residues
Sequence: MTLTKGSFTYSSGEEYRGEWKEGRRHGFGQLVFADGGTYLGHFENGLFNGFGVLTFSDGSRYEGEFSQGKFNGVGVFIRYDNMTFEGEFKNGRVDGFGLLTFPDGSHGIPRNEGLFENNKLLRREKCSAVVQRAQSASKSARNLTA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1608
R free: 0.186
Average B factor: 25.6637
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.6
Crystallization temperature (K): 289
Crystal growth procedure: 0.5 M ammonium sulfate, 1.0 M lithium sulfate, 0.1 M sodium citrate tribasic pH 5.6
Matthews coefficient: 3
Solvent content (%): 59
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: 2019-07-24
Crystal structure of human TAK1/TAB1 fusion protein in complex with ligand 2 (PDB entry 5GJD)
Macromolecule: TAK1 kinase - TAB1 chimera fusion protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 315 residues
Sequence: GPLHMIDYKEIEVEEVVGRGAFGVVCKAKWRAKDVAIKQIESESERKAFIVELRQLSRVNHPNIVKLYGACLNPVCLVMEYAEGGSLYNVLHGAEPLPYYTAAHAMSWCLQCSQGVAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMAPEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCWSKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQHSLPPGEDGRVEPYVDFAEFYRLWSVDHGEQSVVTAP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.1984
R free: 0.2451
Average B factor: 74.242
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.7M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant
Matthews coefficient: 3.85
Solvent content (%): 68.06
Ligand: 1-(4-((1H-pyrrolo[2,3-b]pyridin-4-yl)oxy)phenyl)-3-(5-(4-methylpiperazin-1-yl)naphthalen-2-yl)urea (6V3)
Ligand formula: C29 H28 N6 O2
Ligand molecular weight: 492.572
Ligand SMILES: CN1CCN(CC1)c2cccc3c2ccc(c3)NC(=O)Nc4ccc(cc4)Oc5ccnc6c5cc[nH]6
Ligand InChI: InChI=1S/C29H28N6O2/c1-34-15-17-35(18-16-34)26-4-2-3-20-19-22(7-10-24(20)26)33-29(36)32-21-5-8-23(9-6-21)37-27-12-14-31-28-25(27)11-13-30-28/h2-14,19H,15-18H2,1H3,(H,30,31)(H2,32,33,36)
Release date: 2016-11-16
Human DNA Pol eta S113A with dT-ended primer and dATP: in crystallo reaction for 0 s (PDB entry 7M7T)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERAAIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1792
R free: 0.2081
Average B factor: 22.7045
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 15% PEG 2000 MME,
100 mM MES
Matthews coefficient: 2.11
Solvent content (%): 41.6
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: 2021-06-02
Insight into the molecular recognition mechanism of the coactivator NCoA1 by STAT6 (PDB entry 5NWX)
Macromolecule: Nuclear receptor coactivator 1
Type: Protein, polypeptide(L)
Source organism: Mus musculus
EC number: 2.3.1.48
Sequence length: 132 residues
Sequence: GHMTGVESFMTKQDTTGKIISIDTSSLRAAGRTGWEDLVRKCIYAFFQPQGREPSYARQLFQEVMTRGTASSPSYRFILNDGTMLSAHTRCKLCYPQSPDMQPFIMGIHIIDREHSGLSPQDDTNSGMSIPR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.51
R work: 0.18352
R free: 0.23546
Average B factor: 46.36
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, 30% PEG 8000, 5% PEG 400
Matthews coefficient: 2.25
Solvent content (%): 44.09
Release date: 2017-12-13
HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 3C (PDB entry 7LM2)
Macromolecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.153
Sequence length: 1020 residues
Sequence: WTKEENQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPGTLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRAKPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.79
R work: 0.2405
R free: 0.2895
Average B factor: 97.127
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 12-14% PEG6000, 100 MM MES/NAOH, PH 5.75, 5 MM DTT
Matthews coefficient: 2.7
Solvent content (%): 53.4
Ligand: cyclopropyl[(3S)-3-{[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]amino}pyrrolidin-1-yl]methanone (Y5Y)
Ligand formula: C20 H24 N8 O
Ligand molecular weight: 392.458
Ligand SMILES: CCn1c2c(c(ncn2)NC3CCN(C3)C(=O)C4CC4)nc1c5cnc(nc5)C
Ligand InChI: InChI=1S/C20H24N8O/c1-3-28-18(14-8-21-12(2)22-9-14)26-16-17(23-11-24-19(16)28)25-15-6-7-27(10-15)20(29)13-4-5-13/h8-9,11,13,15H,3-7,10H2,1-2H3,(H,23,24,25)/t15-/m0/s1
Release date: 2021-04-21
Crystal Structure of the Human CAMKK2B bound to GSK650394 (PDB entry 6BKU)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 291 residues
Sequence: SMQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTRH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.19271
R free: 0.23658
Average B factor: 44.588
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.2
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG smear medium, 0.2M sodium formate, 0.1M sodium-potassium phosphate, 10% glycerol
Matthews coefficient: 2.4
Solvent content (%): 48.69
Ligand: 2-cyclopentyl-4-(5-phenyl-1H-pyrrolo[2,3-b]pyridin-3-yl)benzoic acid (DXV)
Ligand formula: C25 H22 N2 O2
Ligand molecular weight: 382.454
Ligand SMILES: c1ccc(cc1)c2cc3c(c[nH]c3nc2)c4ccc(c(c4)C5CCCC5)C(=O)O
Ligand InChI: InChI=1S/C25H22N2O2/c28-25(29)20-11-10-18(12-21(20)17-8-4-5-9-17)23-15-27-24-22(23)13-19(14-26-24)16-6-2-1-3-7-16/h1-3,6-7,10-15,17H,4-5,8-9H2,(H,26,27)(H,28,29)
Release date: 2017-11-29
Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP (PDB entry 5HVJ)
Macromolecule: LIM domain kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 315 residues
Sequence: GAMGSRPHRIFRPSDLIHGEVLGKGCFGQAIKVTHRETGEVMVMKELIRFDEETQRTFLKEVKVMRCLEHPNVLKFIGVLYKDKRLNFITEYIKGGTLRGIIKSMDSQYPWSQRVSFAKDIASGMAYLHSMNIIHRNLNSHNCLVRENKNVVVADFGLARLMVDEKTQPEGLRSLKKPDRKKRYTVVGNPYWMAPEMINGRSYDEKVDVFSFGIVLCEIIGRVNADPDYLPRTMDFGLNVRGFLDRYCPPNCPPSFFPITVRCCDLDPEKRPSFVKLEHWLETLRMHLAGHLPLGPQLEQLDRGFWETYRRGESG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2057
R free: 0.2522
Average B factor: 75.1
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 18-24% PEG 3350, 0.2 M potassium citrate
Matthews coefficient: 2.17
Solvent content (%): 43.28
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: 2016-05-04
Notum-Fragment065 (PDB entry 7B84)
Macromolecule: Palmitoleoyl-protein carboxylesterase NOTUM
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.98
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.36
R work: 0.2137
R free: 0.2259
Average B factor: 21.9708
Crystallization method: EVAPORATION
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M Ammonium Sulphate
0.1 M Sodium Citrate, pH4.2
Matthews coefficient: 1.98
Solvent content (%): 37.82
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: 2022-01-12
Crystal structure of the computationally designed chemically disruptable heterodimer LD6-MDM2 (PDB entry 7AYE)
Macromolecule: Isoform 11 of E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 114 residues
Sequence: MEFSQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVNQQESSDSGTSVSENLE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.1971
R free: 0.2599
Average B factor: 86.097
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.5 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6.5
Matthews coefficient: 2.15
Solvent content (%): 42.89
Release date: 2021-08-18
Crystal structure of human choline alpha in complex with an inhibitor (PDB entry 7NB2)
Macromolecule: Choline kinase alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.32
Sequence length: 384 residues
Sequence: GPQPPADEQPEPRTRRRAYLWCKEFLPGAWRGLREDEFHISVIRGGLSNMLFQCSLPDTTATLGDEPRKVLLRLYGAILQMRSCNKEGSEQAQKENEFQGAEAMVLESVMFAILAERSLGPKLYGIFPQGRLEQFIPSRRLDTEELSLPDISAEIAEKMATFHGMKMPFNKEPKWLFGTMEKYLKEVLRIKFTEESRIKKLHKLLSYNLPLELENLRSLLESTPSPVVFCHNDCQEGNILLLEGRENSEKQKLMLIDFEYSSYNYRGFDIGNHFCEWMYDYSYEKYPFFRANIRKYPTKKQQLHFISSYLPAFQNDFENLSTEEKSIIKEEMLLEVNRFALASHFLWGLWSIVQAKISSIEFGYMDYAQARFDAYFHQKRKLGV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.2017
R free: 0.2477
Average B factor: 62.682
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 18-20% Peg-mme 5000, 0.1 M Magnesium Formate, 0.1 M HEPES pH 7.0.
Matthews coefficient: 2.44
Solvent content (%): 49.5
Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (EPE)
Ligand formula: C8 H18 N2 O4 S
Ligand molecular weight: 238.305
Ligand SMILES: C1CN(CCN1CCO)CCS(=O)(=O)O
Ligand InChI: InChI=1S/C8H18N2O4S/c11-7-5-9-1-3-10(4-2-9)6-8-15(12,13)14/h11H,1-8H2,(H,12,13,14)
Release date: 2021-10-13
CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2218325A (COMPOUND 32) (PDB entry 7A14)
Macromolecule: Methionine aminopeptidase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.11.18
Sequence length: 371 residues
Sequence: GPKVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPTCKEVVSRGDDY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.1791
R free: 0.2147
Average B factor: 40.58
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD)
Matthews coefficient: 2.65
Solvent content (%): 53.61
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: 2020-09-23
RT XFEL structure of CypA solved using celloluse carrier media (PDB entry 6U5E)
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): 1.56
R work: 0.1348
R free: 0.1509
Average B factor: 29.62
Crystallization method: BATCH MODE
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: 100 mM HEPES, pH 7.5, 5 mM TCEP, 20% PEG3350
Matthews coefficient: 2.8
Solvent content (%): 56.02
Release date: 2020-01-29
Crystal Structure of human phosphodiesterase 10 in complex with 3-(2-naphthalen-1-ylpyrazol-3-yl)-1-[3-(trifluoromethoxy)phenyl]pyridazin-4-one (PDB entry 5SI4)
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): 2.39
R work: 0.1749
R free: 0.238
Average B factor: 47.153
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: 2.65
Solvent content (%): 53.66
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
human carbonic anhydrase II bound to an inhibitor modified with azidothymidine (PDB entry 6WKA)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.34
R work: 0.1267
R free: 0.1658
Average B factor: 11.385
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 7.5 MG/ML PROTEIN WITH 2.7 M AMMONIUM SULFATE, 100 MM TRIS PH 8.5 AT 8 C
Matthews coefficient: 2.09
Solvent content (%): 41.06
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: 2021-02-24
Ternary complex crystal structure of DNA polymerase Beta with S-isomer of beta-gamma-CHCL-dCTP (PDB entry 6BEM)
Macromolecule: Template strand
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACGTCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.187
R free: 0.2263
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.25
Solvent content (%): 45.43
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: 2018-10-31