satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human Mps1 (TTK) C604Y mutant in complex with NMS-P715 (PDB entry 5NTT)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 287 residues
Sequence: ENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMEYGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.75
R work: 0.1992
R free: 0.2298
Average B factor: 73.976
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 291
Crystal growth procedure: 10.5% (w/v) PEG 350 MME, 10 mM MgCl2, and 100 mM Tris/HCl
Matthews coefficient: 3.44
Solvent content (%): 64.26
Ligand: N-(2,6-DIETHYLPHENYL)-1-METHYL-8-({4-[(1-METHYLPIPERIDIN-4-YL)CARBAMOYL]-2-(TRIFLUOROMETHOXY)PHENYL}AMINO)-4,5-DIHYDRO-1H-PYRAZOLO[4,3-H]QUINAZOLINE-3-CARBOXAMIDE (SVE)
Ligand formula: C35 H39 F3 N8 O3
Ligand molecular weight: 676.731
Ligand SMILES: CCc1cccc(c1NC(=O)c2c3c(n(n2)C)-c4c(cnc(n4)Nc5ccc(cc5OC(F)(F)F)C(=O)NC6CCN(CC6)C)CC3)CC
Ligand InChI: InChI=1S/C35H39F3N8O3/c1-5-20-8-7-9-21(6-2)28(20)42-33(48)30-25-12-10-23-19-39-34(43-29(23)31(25)46(4)44-30)41-26-13-11-22(18-27(26)49-35(36,37)38)32(47)40-24-14-16-45(3)17-15-24/h7-9,11,13,18-19,24H,5-6,10,12,14-17H2,1-4H3,(H,40,47)(H,42,48)(H,39,41,43)
Release date: 2017-07-26
ASH1L SET domain Q2265A mutant in complex with S-adenosyl methionine (SAM) (PDB entry 4YPA)
Macromolecule: Histone-lysine N-methyltransferase ASH1L
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.43
Sequence length: 226 residues
Sequence: GAMAGSYKKIRSNVYVDVKPLSGYEATTCNCKKPDDDTRKGCVDDCLNRMIFAECSPNTCPCGEQCCNQRIQRHEWVQCLERFRAEEKGWGIRTKEPLKAGQFIIEYLGEVVSEQEFRNRMIEQYHNHSDHYCLNLDSGMVIDSYRMGNEARFINHSCDPNCEMQKWSVNGVYRIGLYALKDMPAGTELTYDYNFHSFNVEKAQLCKCGFEKCRGIIGGKSQRVNG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2489
R free: 0.303
Average B factor: 38.039
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 290
Crystal growth procedure: PEG 4000, magnesium chloride, Tris
Matthews coefficient: 2.34
Solvent content (%): 47.34
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: 2015-09-02
Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II (PDB entry 5XIT)
Macromolecule: Ubiquitin-40S ribosomal protein S27a
Type: Protein, polypeptide(L)
Source organism: Mus musculus
Sequence length: 76 residues
Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQRESTLHLVLRLRGG
Oligomeric state: Hetero 3-mer
Stoichiometry: A2, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.2202
R free: 0.2391
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 23% PEG MME 2000, 0.1 M Bis-Tris (pH 6.5), 10 mM Pr acetate
Matthews coefficient: 2.39
Solvent content (%): 48.58
Ligand: PRASEODYMIUM ION (PR)
Ligand formula: Pr
Ligand molecular weight: 140.908
Ligand SMILES: [Pr+3]
Ligand InChI: InChI=1S/Pr/q+3
Release date: 2018-03-07
Human AURKC INCENP complex bound to VX-680 (PDB entry 6GR9)
Macromolecule: Aurora kinase C
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 274 residues
Sequence: GANSRRLTVDDFEIGRPLGKGKFGNVYLARLKESHFIVALKVLFKSQIEKEGLEHQLRREIEIQAHLQHPNILRLYNYFHDARRVYLILEYAPRGELYKELQKSDKLDEQRTATIIEELADALTYCHDKKVIHRDIKPENLLLGFRGEVKIADFGWSVHTPSLRRKTMCGTLDYLPPEMIEGRTYDEKVDLWCIGVLCYELLVGYPPFESASHSETYRRILKVDVRFPLSMPLGARDLISRLLRYQPLERLPLAQILKHPWVQAHSRRVLPPCA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.18165
R free: 0.22443
Average B factor: 44.179
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 % PEG3350, 10 % ethylene glycol, 0.1 M bis-tris-propane pH 7.5, 0.2 M sodium sulfate
Matthews coefficient: 2.95
Solvent content (%): 58.24
Ligand: CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE (VX6)
Ligand formula: C23 H28 N8 O S
Ligand molecular weight: 464.586
Ligand SMILES: Cc1cc([nH]n1)Nc2cc(nc(n2)Sc3ccc(cc3)NC(=O)C4CC4)N5CCN(CC5)C
Ligand InChI: InChI=1S/C23H28N8OS/c1-15-13-20(29-28-15)25-19-14-21(31-11-9-30(2)10-12-31)27-23(26-19)33-18-7-5-17(6-8-18)24-22(32)16-3-4-16/h5-8,13-14,16H,3-4,9-12H2,1-2H3,(H,24,32)(H2,25,26,27,28,29)
Release date: 2019-05-15
Human asparagine synthetase (ASNS) in complex with 6-diazo-5-oxo-L-norleucine (DON) at 1.85 A resolution (PDB entry 6GQ3)
Macromolecule: Asparagine synthetase [glutamine-hydrolyzing]
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.5.4
Sequence length: 561 residues
Sequence: MCGIWALFGSDDCLSVQCLSAMKIAHRGPDAFRFENVNGYTNCCFGFHRLAVVDPLFGMQPIRVKKYPYLWLCYNGEIYNHKKMQQHFEFEYQTKVDGEIILHLYDKGGIEQTICMLDGVFAFVLLDTANKKVFLGRDTYGVRPLFKAMTEDGFLAVCSEAKGLVTLKHSATPFLKVEPFLPGHYEVLDLKPNGKVASVEMVKYHHCRDVPLHALYDNVEKLFPGFEIETVKNNLRILFNNAVKKRLMTDRRIGCLLSGGLDSSLVAATLLKQLKEAQVQYPLQTFAIGMEDSPDLLAARKVADHIGSEHYEVLFNSEEGIQALDEVIFSLETYDITTVRASVGMYLISKYIRKNTDSVVIFSGEGSDELTQGYIYFHKAPSPEKAEEESERLLRELYLFDVLRADRTTAAHGLELRVPFLDHRFSSYYLSLPPEMRIPKNGIEKHLLRETFEDSNLIPKEILWRPKEAFSDGITSVKNSWFKILQEYVEHQVDDAMMANAAQKFPFNTPKTKEGYYYRQVFERHYPGRADWLSHYWMPKWINATDPSARTLTHYKSAVKA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.17764
R free: 0.22462
Average B factor: 33.556
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 290
Crystal growth procedure: 0.2 M NaCl, 0.1 M sodium HEPES buffer, pH 7.5, and 12% w/v PEG 8000
Matthews coefficient: 2.31
Solvent content (%): 46.79
Ligand: 5-OXO-L-NORLEUCINE (ONL)
Ligand formula: C6 H11 N O3
Ligand molecular weight: 145.156
Ligand SMILES: CC(=O)CCC(C(=O)O)N
Ligand InChI: InChI=1S/C6H11NO3/c1-4(8)2-3-5(7)6(9)10/h5H,2-3,7H2,1H3,(H,9,10)/t5-/m0/s1
Release date: 2019-09-18
Structure of HDAC2 in complex with an inhibitor (compound 14) (PDB entry 7MOX)
Macromolecule: Histone deacetylase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.98
Sequence length: 376 residues
Sequence: MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.176
R free: 0.2021
Average B factor: 27.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5
Matthews coefficient: 2.48
Solvent content (%): 50.47
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: 2021-07-14
Crystal structure of the PWWP1 domain of NSD2 bound by compound 34. (PDB entry 9EXY)
Macromolecule: Histone-lysine N-methyltransferase NSD2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.357
Sequence length: 182 residues
Sequence: MGGGPNTGRDKDHLLKYNVGDLVWSKVSGYPWWPCMVSADPLLHSYTKLKGQAASARQYHVQFFGDAPERAWIFEKSLVAFEGEGQFEKLCQESAKQAPTAAEKIKLLAPISGKLRAQWEMGIVQAEEAASMSVEERKAKFTFLYVGDQLHLNPQVAKEAGIAAEGGGENLYFQGSHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.699
R work: 0.2214
R free: 0.2479
Average B factor: 41.59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: Morpheus screen, condition G9
Matthews coefficient: 2.33
Solvent content (%): 47.15
Ligand: 7-[5-methyl-3-[2-methyl-5-(piperidin-1-ylmethyl)phenyl]-1,2-oxazol-4-yl]-4~{H}-1,4-benzoxazin-3-one (A1H7Z)
Ligand formula: C25 H27 N3 O3
Ligand molecular weight: 417.5
Ligand SMILES: Cc1ccc(cc1c2c(c(on2)C)c3ccc4c(c3)OCC(=O)N4)CN5CCCCC5
Ligand InChI: InChI=1S/C25H27N3O3/c1-16-6-7-18(14-28-10-4-3-5-11-28)12-20(16)25-24(17(2)31-27-25)19-8-9-21-22(13-19)30-15-23(29)26-21/h6-9,12-13H,3-5,10-11,14-15H2,1-2H3,(H,26,29)
Release date: 2024-05-29
Crystal structure of nanobody/VHH domain of 34E5 in complex with the extracellular region of the epidermal growth factor variant III (EGFRvIII) (PDB entry 8UKV)
Macromolecule: Nanobody/VHH domain 34E5
Type: Protein, polypeptide(L)
Source organism: Lama glama
Sequence length: 141 residues
Sequence: EVQLVESGGGLVQPGGSLRLSCTASGMIFSFNVMGWYRQAPGNQRELAATITTDGSTNYADSVKGRFTISRDKNTVYLQMNSLKPEDTAVYYCHLKNIRDYRNYSNYWGQGTQVTVSSAAAEQKLISEEDLNGLEHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.94
R work: 0.2149
R free: 0.2524
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 70-90 micromolar protein, 15-20% PEG 3350, 100 mM ammonium phosphate, pH 7.4,  +20% PEG400 for cryo
Matthews coefficient: 3.89
Solvent content (%): 68.35
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: 2024-06-19
Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with EGR-chloromethylketone (PDB entry 5JBB)
Macromolecule: Coagulation factor IX
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.22
Sequence length: 58 residues
Sequence: CNIKNGRCEQFCKNSADNKVVCSCTEGYRLAENQKSCEPAVPFPCGRVSVSQTSKLTR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.1582
R free: 0.1901
Average B factor: 36.2923
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 6 mg/mL protein-inhibitor complex, 
0.1M MES pH 6.5, 
20% PEG6000
Matthews coefficient: 2.2
Solvent content (%): 44.18
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: 2016-06-01
Crystal structure of human CLK1 in complex with Leucettinib-21 (PDB entry 8P08)
Macromolecule: Dual specificity protein kinase CLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 339 residues
Sequence: SMHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLKKSI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.209
R free: 0.26
Average B factor: 51.12
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG 3350
0.2M Na malonate pH 7
Matthews coefficient: 2.58
Solvent content (%): 52.25
Ligand: (4~{Z})-4-(1,3-benzothiazol-6-ylmethylidene)-2-[[(2~{R})-1-methoxy-4-methyl-pentan-2-yl]amino]-1~{H}-imidazol-5-one (WAZ)
Ligand formula: C18 H22 N4 O2 S
Ligand molecular weight: 358.458
Ligand SMILES: CC(C)CC(COC)NC1=NC(=Cc2ccc3c(c2)scn3)C(=O)N1
Ligand InChI: InChI=1S/C18H22N4O2S/c1-11(2)6-13(9-24-3)20-18-21-15(17(23)22-18)7-12-4-5-14-16(8-12)25-10-19-14/h4-5,7-8,10-11,13H,6,9H2,1-3H3,(H2,20,21,22,23)/b15-7-/t13-/m1/s1
Release date: 2023-05-17
Zn-Carbonic Anhydrase II complexed with 3NPA before UV at 90 K (PDB entry 7Y2A)
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): 1.2
R work: 0.12708
R free: 0.15578
Average B factor: 12.026
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 50 mM Tris-HCl
Matthews coefficient: 2.08
Solvent content (%): 40.74
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2023-12-20
Crystal structure of a yeast SAGA transcriptional coactivator Ada2/Gcn5 HAT subcomplex, crystal form 1 (PDB entry 6CW2)
Macromolecule: Histone acetyltransferase GCN5
Type: Protein, polypeptide(L)
Source organism: Saccharomyces cerevisiae S288C
EC number: 2.3.1.48
Sequence length: 251 residues
Sequence: VTDVEKGIVKFEFDGVEYTFKERPSVVEENEGKIEFRVVNNDNTKENMMVLTGLKNIFQKQLPKMPKEYIARLVYDRSHLSMAVIRKPLTVVGGITYRPFDKREFAEIVFCAISSTEQVRGYGAHLMNHLKDYVRNTSNIKYFLTYADNYAIGYFKKQGFTKEITLDKSIWMGYIKDYEGGTLMQCSMLPRIRYLDAGKILLLQEAALRRKIRTISKSHIVRPGLEQFKDLNNIKPIDPMTIPGLKEAGWT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.67
R work: 0.2501
R free: 0.2838
Average B factor: 86.9959
Crystallization method: MICROBATCH
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 10 mM Tris-Cl pH 8.5, 200 mM Li2SO4, 25% w/v PEG3350
Matthews coefficient: 5.52
Solvent content (%): 77.72
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: 2018-09-19
Crystal Structure of PRL-1 complex with compound analogy 3 (PDB entry 5BX1)
Macromolecule: Protein tyrosine phosphatase type IVA 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 157 residues
Sequence: MNRPAPVEVTYKNMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTLVEKEGIHVLDWPFDDGAPPSNQIVDDWLSLVKIKFREEPGCCIAVHCVAGLGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFNSKQLLYLEKYRPKMRLRF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.195
R free: 0.24
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 310
Crystal growth procedure: 1.9 M amino sulfate, 100 mM sodium acetate, pH 4.6 ~ 4.9
Matthews coefficient: 2.17
Solvent content (%): 43.32
Ligand: 3-(5,6-dimethyl-2H-isoindol-2-yl)-N'-[(E)-furan-2-ylmethylidene]benzohydrazide (4XA)
Ligand formula: C22 H19 N3 O2
Ligand molecular weight: 357.405
Ligand SMILES: Cc1cc2cn(cc2cc1C)c3cccc(c3)C(=O)NN=Cc4ccco4
Ligand InChI: InChI=1S/C22H19N3O2/c1-15-9-18-13-25(14-19(18)10-16(15)2)20-6-3-5-17(11-20)22(26)24-23-12-21-7-4-8-27-21/h3-14H,1-2H3,(H,24,26)/b23-12+
Release date: 2016-12-21
Structure of the S167H mutant of human indoleamine 2,3 dioxygenase in complex with tryptophan and cyanide (PDB entry 6CXU)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 425 residues
Sequence: MSKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVHLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEGKGELNSKLEGKPIPNPLLGLDSTRTGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.49
R work: 0.2012
R free: 0.24955
Average B factor: 90.902
Crystallization method: BATCH MODE
Crystallization pH: 10
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M sodium thiosulfate, 0.1 M CAPS, pH 10, 20% PEG8000
Matthews coefficient: 2.88
Solvent content (%): 57.24
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2018-06-27
HUMAN CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 4,5,6,7-TETRABROMOBENZOTRIAZOLE (tBBT) (PDB entry 6TLL)
Macromolecule: Casein kinase II subunit alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 399 residues
Sequence: MSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIELDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.88
R work: 0.1597
R free: 0.187
Average B factor: 46.177
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 290
Crystal growth procedure: 0.1 M sodium HEPES/MOPS buffer pH 7.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 monomethyl ester, 10% polyethylene glycol 20000
Matthews coefficient: 2.68
Solvent content (%): 54.05
Ligand: 4,5,6,7-TETRABROMOBENZOTRIAZOLE (TBS)
Ligand formula: C6 H Br4 N3
Ligand molecular weight: 434.708
Ligand SMILES: c12c(c(c(c(c1Br)Br)Br)Br)nn[nH]2
Ligand InChI: InChI=1S/C6HBr4N3/c7-1-2(8)4(10)6-5(3(1)9)11-13-12-6/h(H,11,12,13)
Release date: 2020-12-16
STRUCTURE OF THE WNT DEACYLASE NOTUM - CRYSTAL FORM VII - SOS COMPLEX - 2.2A (PDB entry 4UZ9)
Macromolecule: PROTEIN NOTUM HOMOLOG
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.1
Sequence length: 383 residues
Sequence: ETGSAQQLNEDLRLHLLLNTSVTCNDGSPAGYYLKESRGSRRWLLFLEGGWYCFNRENCDSRYDTMRRLMSSRDWPRTRTGTGILSSQPEENPYWWNANMVFIPYCSSDVWSGASSKSEKNEYAFMGALIIQEVVRELLGRGLSGAKVLLLAGSSAGGTGVLLNVDRVAEQLEKLGYPAIQVRGLADSGWFLDNKQYRHTDCVDTITCAPTEAIRRGIRYWNGVVPERCRRQFQEGEEWNCFFGYKVYPTLRSPVFVVQWLFDEAQLTVDNVHLTGQPVQEGLRLYIQNLGRELRHTLKDVPASFAPACLSHEIIIRSHWTDVQVKGTSLPRALHCWDRSLHDSHKASKTPLKGCPVHLVDSCPWPHCNPSCPTGTKHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.19007
R free: 0.23653
Average B factor: 39.04
Crystallization pH: 6.5
Crystal growth procedure: 200 MM AMMONIUM SULFATE 100 MM MES 6.5 35 % W/V PEP 629 20MM SOS
Matthews coefficient: 2.7
Solvent content (%): 55
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: 2015-02-25
PanDDA analysis group deposition -- Crystal structure of PTP1B in complex with FMOCR000171b (PDB entry 7FQW)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.17
R work: 0.1862
R free: 0.2329
Average B factor: 45.666
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M HEPES, 0.3 M magnesium acetate, 13.5% PEG 8000, 2% ethanol, and 1 mM BME
Matthews coefficient: 3.3
Solvent content (%): 62.73
Ligand: 2-(thiophen-2-yl)-1H-imidazole (JG4)
Ligand formula: C7 H6 N2 S
Ligand molecular weight: 150.201
Ligand SMILES: c1cc(sc1)c2[nH]ccn2
Ligand InChI: InChI=1S/C7H6N2S/c1-2-6(10-5-1)7-8-3-4-9-7/h1-5H,(H,8,9)
Release date: 2022-11-23
ATAD2 in complex with FragLite3 (PDB entry 7PPX)
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): 1.35
R work: 0.2108
R free: 0.2306
Average B factor: 32.546
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M HEPES pH 7.0, 2.4 AmSO4, ATAD2~5 mg mL-1.
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: 2022-09-21