satarupa22/MacromolecularLigandDB huggingface dataset:
Phospho-ERK2 bound to AMP-PCP (PDB entry 5V60)
Macromolecule: Mitogen-activated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 356 residues
Sequence: GPGGAGPEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYRS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.18
R work: 0.1906
R free: 0.2262
Average B factor: 52.442
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris pH 6.5, 45% v/v polypropylene glycol P400
Matthews coefficient: 3.07
Solvent content (%): 59.99
Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER (ACP)
Ligand formula: C11 H18 N5 O12 P3
Ligand molecular weight: 505.208
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
Ligand InChI: InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
Release date: 2017-07-26
XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010942a (PDB entry 5S7V)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.31
R work: 0.1532
R free: 0.1722
Average B factor: 17.441
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Matthews coefficient: 2.59
Solvent content (%): 52.48
Ligand: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine (LU8)
Ligand formula: C27 H32 N2 O3
Ligand molecular weight: 432.555
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H32N2O3/c1-18-23(21-8-6-19(7-9-21)20-10-12-29(2)13-11-20)16-28-17-24(18)22-14-25(30-3)27(32-5)26(15-22)31-4/h6-9,14-17,20H,10-13H2,1-5H3
Release date: 2021-06-23
PCSK9(deltaCRD) in complex with cyclic peptide 83 (PDB entry 6XIF)
Macromolecule: Proprotein convertase subtilisin/kexin type 9
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21
Sequence length: 122 residues
Sequence: QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.774
R work: 0.1867
R free: 0.2037
Average B factor: 32.32
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: 20% PEG3350, 200mM CaCl2, 100mM MES pH 6
Matthews coefficient: 2.49
Solvent content (%): 50.63
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2020-11-18
The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-1 (PDB entry 5F8Z)
Macromolecule: Plasma kallikrein LIGHT CHAIN
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.34
Sequence length: 239 residues
Sequence: IVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPISLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.17933
R free: 0.21747
Average B factor: 19.358
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: 28% PEG 3350, 0.1M TRIS-HCL PH8.5, 20MM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Matthews coefficient: 2.42
Solvent content (%): 49.09
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2016-12-14
Crystal structure of human ligase I with nick duplexes containing cognate A:T (PDB entry 7SUM)
Macromolecule: DNA(5'-P*GP*TP*CP*GP*GP*AP*C-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 7 residues
Sequence: GTCGGAC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.18
R free: 0.227
Average B factor: 53.89
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, pH 6.6, 100 mM lithium acetate, 20% w/v PEG3350
Matthews coefficient: 2.87
Solvent content (%): 57.13
Ligand: ADENOSINE MONOPHOSPHATE (AMP)
Ligand formula: C10 H14 N5 O7 P
Ligand molecular weight: 347.221
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Ligand InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2022-07-13
X-ray structure of furin in complex with the dichlorophenylpyridine-based inhibitor 4 (PDB entry 7QY1)
Macromolecule: Furin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.75
Sequence length: 480 residues
Sequence: DVYQEPTDPKFPQQWYLSGVTQRDLNVKAAWAQGYTGHGIVVSILDDGIEKNHPDLAGNYDPGASFDVNDQDPDPQPRYTQMNDNRHGTRCAGEVAAVANNGVCGVGVAYNARIGGVRMLDGEVTDAVEARSLGLNPNHIHIYSASWGPEDDGKTVDGPARLAEEAFFRGVSQGRGGLGSIFVWASGNGGREHDSCNCDGYTNSIYTLSISSATQFGNVPWYSEACSSTLATTYSSGNQNEKQIVTTDLRQKCTESHTGTSASAPLAAGIIALTLEANKNLTWRDMQHLVVQTSKPAHLNANDWATNGVGRKVSHSYGYGLLDAGAMVALAQNWTTVAPQRKCIIDILTEPKDIGKRLEVRKTVTACLGEPNHITRLEHAQARLTLSYNRRGDLAIHLVSPMGTRSTLLAARPHDYSADGFNDWAFMTTHSWDEDPSGEWVLEIENTSEANNYGTLTKFTLVLYGTASGSLVPRGSHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1502
R free: 0.1754
Average B factor: 25.78
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: CRYSTALLIZATION SOLUTION: 100mM MES, 200mM K/NAH2PO4, PH 5.5, 2 M NACL; RESERVOIR SOLUTION: 3.0-3.2M NACL
Ligand: 3-[4-[5-[4-[[4-(acetamidomethyl)piperidin-1-ium-1-yl]methyl]-6-[3,5-bis(chloranyl)phenyl]pyridin-2-yl]oxypyridin-2-yl]piperazin-1-ium-1-yl]propanoate (I0W)
Ligand formula: C32 H39 Cl2 N6 O4
Ligand molecular weight: 642.596
Ligand SMILES: CC(=O)NCC1CC[NH+](CC1)Cc2cc(nc(c2)Oc3ccc(nc3)N4CC[NH+](CC4)CCC(=O)[O-])c5cc(cc(c5)Cl)Cl
Ligand InChI: InChI=1S/C32H38Cl2N6O4/c1-22(41)35-19-23-4-7-39(8-5-23)21-24-14-29(25-16-26(33)18-27(34)17-25)37-31(15-24)44-28-2-3-30(36-20-28)40-12-10-38(11-13-40)9-6-32(42)43/h2-3,14-18,20,23H,4-13,19,21H2,1H3,(H,35,41)(H,42,43)/p+1
Release date: 2022-04-20
SdeA DUB Domain in complex with Ubiquitin (PDB entry 6WTG)
Macromolecule: Ubiquitinating/deubiquitinating enzyme SdeA
Type: Protein, polypeptide(L)
Source organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
EC number: 3.4.22
Sequence length: 193 residues
Sequence: MPKYVEGVELTQEGMHAIFARMGYGDITSGSIYNGVPTIDTGALNRQGFMPVLTGVGPHRDSGHWIMLIKGPGNQYYLFDPLGKTSGEGYQNILAAQLPMGSTLSVIPNGSGLNMGLAGYWVASAGLRAHQALNQHNPPTLLNVGQTITNEMRNELDHDGYRKITGWLRAVADEFPEGDPQLDGKALRENTEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.63
R work: 0.204
R free: 0.2428
Average B factor: 37.02
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M bicine pH 9.0, 65% (v/v) MPD
Matthews coefficient: 2.32
Solvent content (%): 47
Release date: 2021-03-03
Homo sapiens FKBP12 protein bound with APX879 in P32 space group (PDB entry 6VCU)
Macromolecule: Peptidyl-prolyl cis-trans isomerase FKBP1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 111 residues
Sequence: GSHMGVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELLKLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1559
R free: 0.1955
Average B factor: 15.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 293
Crystal growth procedure: 2.5M Ammonium sulfate, 0.1M Sodium acetate trihydrate
Matthews coefficient: 2.2
Solvent content (%): 44.03
Ligand: ACETATE ION (ACT)
Ligand formula: C2 H3 O2
Ligand molecular weight: 59.044
Ligand SMILES: CC(=O)[O-]
Ligand InChI: InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)/p-1
Release date: 2020-12-16
Discovery of VX-509 (Decernotinib): A Potent and Selective Janus kinase (JAK) 3 Inhibitor for the Treatment of Autoimmune Diseases (PDB entry 4YTF)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 296 residues
Sequence: GSHNMTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.78
R work: 0.1825
R free: 0.2132
Average B factor: 27.68
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.7-2.1 M DL-malic acid pH 7.0, 2mM DTT
Matthews coefficient: 2.33
Solvent content (%): 47.22
Ligand: N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-N-(2,2,2-trifluoroethyl)-L-alaninamide (4HZ)
Ligand formula: C16 H13 Cl F4 N6 O
Ligand molecular weight: 416.761
Ligand SMILES: CC(C(=O)NCC(F)(F)F)Nc1c(cnc(n1)c2c[nH]c3c2cc(cn3)Cl)F
Ligand InChI: InChI=1S/C16H13ClF4N6O/c1-7(15(28)25-6-16(19,20)21)26-14-11(18)5-24-13(27-14)10-4-23-12-9(10)2-8(17)3-22-12/h2-5,7H,6H2,1H3,(H,22,23)(H,25,28)(H,24,26,27)/t7-/m0/s1
Release date: 2015-08-12
Crystal structure of human holo SepSecS (PDB entry 7L1T)
Macromolecule: O-phosphoseryl-tRNA(Sec) selenium transferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.9.1.2
Sequence length: 521 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMNRESFAAGERLVSPAYVRQGCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAIMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASPSLDVLITLLSLGSNGYKKLLKERKEMFSYLSNQIKKLSEAYNERLLHTPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFRGFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRKERSKESDDNYDKTEDVDIEEMALKLDNVLLDTYQDASS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.25
R work: 0.1919
R free: 0.2295
Average B factor: 65.4207
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.3
Crystallization temperature (K): 285
Crystal growth procedure: 0.36 M lithium citrate, 15% PEG 3,350, 0.1 M sodium cacodylic acid, 0.04 M HCl

4 mg/mL SepSecS, 1 mg/mL human tRNASec
Matthews coefficient: 2.26
Solvent content (%): 45.48
Ligand: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE (PLR)
Ligand formula: C8 H12 N O5 P
Ligand molecular weight: 233.158
Ligand SMILES: Cc1c(cnc(c1O)C)COP(=O)(O)O
Ligand InChI: InChI=1S/C8H12NO5P/c1-5-7(4-14-15(11,12)13)3-9-6(2)8(5)10/h3,10H,4H2,1-2H3,(H2,11,12,13)
Release date: 2022-02-09
Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative (PDB entry 6T54)
Macromolecule: Prothrombin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.5
Sequence length: 36 residues
Sequence: TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.57
R work: 0.1377
R free: 0.1702
Average B factor: 22.46
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 20 mM NaH2PO4, 350 mM NaCl, 27% (w/v) PEG8000
Matthews coefficient: 2.54
Solvent content (%): 51.51
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2020-11-18
Human PFKFB3 in complex with a N-Aryl 6-Aminoquinoxaline inhibitor 2 (PDB entry 6HVI)
Macromolecule: 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.105
Sequence length: 520 residues
Sequence: MPLELTQSRVQKIWVPVDHRPSLPRSCGPKLTNSPTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFNVGEYRREAVKQYSSYNFFRPDNEEAMKVRKQCALAALRDVKSYLAKEGGQIAVFDATNTTRERRHMILHFAKENDFKAFFIESVCDDPTVVASNIMEVKISSPDYKDCNSAEAMDDFMKRISCYEASYQPLDPDKCDRDLSLIKVIDVGRRFLVNRVQDHIQSRIVYYLMNIHVQPRTIYLCRHGENEHNLQGRIGGDSGLSSRGKKFASALSKFVEEQNLKDLRVWTSQLKSTIQTAEALRLPYEQWKALNEIDAGVCEELTYEEIRDTYPEEYALREQDKYYYRYPTGESYQDLVQRLEPVIMELERQENVLVICHQAVLRCLLAYFLDKSAEEMPYLKCPLHTVLKLTPVAYGCRVESIYLNVESVCTHRERSEDAKKGPNPLMRRNSVTPLASPEPTKKPRINSFEEHVASTSAALPSCLPPEVPTQLPGQNMKGSRSSADSSRKH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1863
R free: 0.2084
Average B factor: 31.937
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.16M Monosaccharides, 30% GOL_P4K, 0.1M MOPS/Hepes pH 7.5
Matthews coefficient: 3.88
Solvent content (%): 68.32
Ligand: 8-[3-(dimethylamino)phenyl]-~{N}-(4-methylsulfonylpyridin-3-yl)quinoxalin-6-amine (GV5)
Ligand formula: C22 H21 N5 O2 S
Ligand molecular weight: 419.499
Ligand SMILES: CN(C)c1cccc(c1)c2cc(cc3c2nccn3)Nc4cnccc4S(=O)(=O)C
Ligand InChI: InChI=1S/C22H21N5O2S/c1-27(2)17-6-4-5-15(11-17)18-12-16(13-19-22(18)25-10-9-24-19)26-20-14-23-8-7-21(20)30(3,28)29/h4-14,26H,1-3H3
Release date: 2018-11-14
Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment (3R)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol (N10057a) (ligand modelled based on PANDDA event map, SGC - Diamond I04-1 fragment screening) (PDB entry 5FZ4)
Macromolecule: LYSINE-SPECIFIC DEMETHYLASE 5B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 479 residues
Sequence: SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPFACDVDKLHFTPRIQRLNELEAQTRVKLGGGGARDYTLRTFGEMADAFKSDYFNMPVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKLSPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLRAESYNEWALNVNEALEAKI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.1984
R free: 0.2343
Crystallization pH: 7.5
Crystal growth procedure: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Matthews coefficient: 2.1
Solvent content (%): 41.4
Ligand: (3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol (P6B)
Ligand formula: C13 H15 N3 O2
Ligand molecular weight: 245.277
Ligand SMILES: c1ccc(cc1)c2nc(on2)CN3CCC(C3)O
Ligand InChI: InChI=1S/C13H15N3O2/c17-11-6-7-16(8-11)9-12-14-13(15-18-12)10-4-2-1-3-5-10/h1-5,11,17H,6-9H2/t11-/m0/s1
Release date: 2016-03-23
Structure of Ku80 von Willebrand domain S229A mutant complexed with APLF and XLF Ku Binding Motif (PDB entry 6TYT)
Macromolecule: X-ray repair cross-complementing protein 5
Type: Protein, polypeptide(L)
Source organism: Xenopus laevis
EC number: 3.6.4
Sequence length: 231 residues
Sequence: MHHHHHHMARAAKSAVVLCMDVGLAMSHSNQGKESPFEQAKKVMMLFLQRQVFAESKDEIAVVLYGTDTTDNALAREDQYENISVHRHLMLPDFDLLEQIENVVEPGSVQADFLDALIVSMDLLQKETLGKKYTRLHIAVFSDLSSPFSVDQLEVIIANLKKAEITLQFFLPFSVDEGSGPGKGLSDQQKEGIEMVRKIMFSLDGEEGLSEVFTFRDALERLSIFKKIERR
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.40348787647
R work: 0.22504942686
R free: 0.259533479025
Average B factor: 83.3805343643
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M HEPES NaOH pH 7.5, 25 % (w/v) PEG3350
Matthews coefficient: 1.99
Solvent content (%): 38.07
Release date: 2019-11-27
uPA-NU-09F (PDB entry 5ZC5)
Macromolecule: Urokinase-type plasminogen activator chain B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.73
Sequence length: 253 residues
Sequence: IIGGEFTTIENQPWFAAIYRRHRGGSVTYVCGGSLISPCWVISATHCFIDYPKKEDYIVYLGRSRLNSNTQGEMKFEVENLILHKDYSADTLAHHNDIALLKIRSKEGRCAQPSRTIQTIALPSMYNDPQFGTSCEITGFGKEQSTDYLYPEQLKMTVVKLISHRECQQPHYYGSEVTTKMLCAADPQWKTDSCQGDSGGPLVCSLQGRMTLTGIVSWGRGCALKDKPGVYTRVSHFLPWIRSHTKEENGLAL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.203
R free: 0.235
Average B factor: 37.68
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 50mM sodium citrate pH 4.6, 1.95M (NH4)2SO4, 0.03% NaN3, 5% PEG 400
Matthews coefficient: 2.17
Solvent content (%): 43.4
Ligand: 3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-(4-fluoranyl-1-benzofuran-2-yl)pyrazine-2-carboxamide (09I)
Ligand formula: C20 H22 F N7 O2
Ligand molecular weight: 411.433
Ligand SMILES: c1cc2c(cc(o2)c3c(nc(c(n3)C(=O)NC(=N)N)N)N4CCCCCC4)c(c1)F
Ligand InChI: InChI=1S/C20H22FN7O2/c21-12-6-5-7-13-11(12)10-14(30-13)15-18(28-8-3-1-2-4-9-28)26-17(22)16(25-15)19(29)27-20(23)24/h5-7,10H,1-4,8-9H2,(H2,22,26)(H4,23,24,27,29)
Release date: 2018-12-19
MAP4K4 Bound to inhibitor compound 1 (PDB entry 4U41)
Macromolecule: Mitogen-activated protein kinase kinase kinase kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 332 residues
Sequence: GSANDSPAKSLVDIDLSSLRDPAGIFELVEVVGNGTYGQVYKGRHVKTGQLAAIKVMDVTEDEEEEIKLEINMLKKYSHHRNIATYYGAFIKKSPPGHDDQLWLVMEFCGAGSITDLVKNTKGNTLKEDWIAYISREILRGLAHLHIHHVIHRDIKGQNVLLTENAEVKLVDFGVSAQLDRTVGRRNTFIGTPYWMAPEVIACDENPDATYDYRSDLWSCGITAIEMAEGAPPLCDMHPMRALFLIPRNPPPRLKSKKWSKKFFSFIEGCLVKNYMQRPSTEQLLKHPFIRDQPNERQVRIQLKDHIDRTRKKRGEKDETEYEYSGSEEGNS
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.1998
R free: 0.2593
Average B factor: 44.2669
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 292
Crystal growth procedure: 0.2 M potassium citrate, pH 8.3, 20% PEG 3350
Matthews coefficient: 2
Solvent content (%): 38.54
Ligand: 6-[(3S)-3-(4-methyl-1H-pyrazol-3-yl)piperidin-1-yl]pyrido[3,2-d]pyrimidin-4-amine (3C8)
Ligand formula: C16 H19 N7
Ligand molecular weight: 309.369
Ligand SMILES: Cc1c[nH]nc1C2CCCN(C2)c3ccc4c(n3)c(ncn4)N
Ligand InChI: InChI=1S/C16H19N7/c1-10-7-20-22-14(10)11-3-2-6-23(8-11)13-5-4-12-15(21-13)16(17)19-9-18-12/h4-5,7,9,11H,2-3,6,8H2,1H3,(H,20,22)(H2,17,18,19)/t11-/m0/s1
Release date: 2016-01-06
PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001569a (PDB entry 5RB6)
Macromolecule: Lysine-specific demethylase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11
Sequence length: 372 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLKSELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRLRSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRLNLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNVMVYVGIPIGEGAHDEEVLKTIDEGDADEVTKERIHDHKEKPGALWHIYAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYEEYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKHCFRLTQEFRHLSNTHT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.63
R work: 0.1819
R free: 0.2077
Average B factor: 29.677
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M bis-tris pH 5.5 21% PEG3350  0.3M magnesium chloride
Matthews coefficient: 2.8
Solvent content (%): 56.1
Ligand: 1-(4-chlorophenyl)-3-(2-methyl-1-oxidanyl-propan-2-yl)urea (S9V)
Ligand formula: C11 H15 Cl N2 O2
Ligand molecular weight: 242.702
Ligand SMILES: CC(C)(CO)NC(=O)Nc1ccc(cc1)Cl
Ligand InChI: InChI=1S/C11H15ClN2O2/c1-11(2,7-15)14-10(16)13-9-5-3-8(12)4-6-9/h3-6,15H,7H2,1-2H3,(H2,13,14,16)
Release date: 2020-04-22
Crystal structure of MMP12 mutant K421A in complex with RXP470.1 conjugated with fluorophore Cy5,5 in space group P21. (PDB entry 5L7F)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYAYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1756
R free: 0.19464
Average B factor: 21.924
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 293
Crystal growth procedure: protein: MMP12-F171D-K241A  661 micro-M + 10 milli-M AHA, 10% DMSO, 0.5 milli-M fluorescent inhibitor (R47-CY5)
precipitant: 20% PEG4K, 2% gamma valerolactone, 0.2 milli-M TRIS pH 9.5
40% CM26 ((12.5 % diethylene glycol + 12.5 % ethylene glycol + 12.5 % glycerol + 25 % 2,3-butanediol + 12.5 % DMSO), 25% MPEG 6K
Matthews coefficient: 2.48
Solvent content (%): 50.34
Ligand: BROMIDE ION (BR)
Ligand formula: Br
Ligand molecular weight: 79.904
Ligand SMILES: [Br-]
Ligand InChI: InChI=1S/BrH/h1H/p-1
Release date: 2016-09-14