satarupa22/MacromolecularLigandDB huggingface dataset:
Small Molecule inhibitors of IAP (PDB entry 5M6L)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 127 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.61
R work: 0.197
R free: 0.263
Average B factor: 43.55
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 277
Crystal growth procedure: 3.3M NaCl
.1M pH=8 HEPES/NaOH
Matthews coefficient: 4.62
Solvent content (%): 73.4
Ligand: 1-[6-[(4-fluorophenyl)methyl]-3,3-dimethyl-2~{H}-pyrrolo[3,2-b]pyridin-1-yl]-2-[(2~{R},5~{R})-5-methyl-2-[[(3~{R})-3-methylmorpholin-4-yl]methyl]piperazin-4-ium-1-yl]ethanone (7H9)
Ligand formula: C29 H41 F N5 O2
Ligand molecular weight: 510.667
Ligand SMILES: CC1CN(C(C[NH2+]1)CN2CCOCC2C)CC(=O)N3CC(c4c3cc(cn4)Cc5ccc(cc5)F)(C)C
Ligand InChI: InChI=1S/C29H40FN5O2/c1-20-15-34(25(14-31-20)16-33-9-10-37-18-21(33)2)17-27(36)35-19-29(3,4)28-26(35)12-23(13-32-28)11-22-5-7-24(30)8-6-22/h5-8,12-13,20-21,25,31H,9-11,14-19H2,1-4H3/p+1/t20-,21-,25-/m1/s1
Release date: 2017-05-24
Crystal Structure of the Jak3 Kinase Domain Covalently Bound to N-(3-(((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)pyrimidin-4-yl)amino)methyl)phenyl)acrylamide (PDB entry 4Z16)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 316 residues
Sequence: GSCQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRPELRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGCERDVPALCRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSRGCETHAFTAHPEGKHHSLSFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2021
R free: 0.2401
Average B factor: 65.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-tris pH 6.5, 16% PEG 3350, 0.2 M ammonium sulfate, 5 mM TCEP
Matthews coefficient: 2.71
Solvent content (%): 54.54
Ligand: N-(3-{[(5-chloro-2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}pyrimidin-4-yl)amino]methyl}phenyl)prop-2-enamide (4LH)
Ligand formula: C26 H30 Cl N7 O2
Ligand molecular weight: 508.015
Ligand SMILES: CN1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc(c(n3)NCc4cccc(c4)NC(=O)C=C)Cl
Ligand InChI: InChI=1S/C26H30ClN7O2/c1-4-24(35)30-19-7-5-6-18(14-19)16-28-25-21(27)17-29-26(32-25)31-22-9-8-20(15-23(22)36-3)34-12-10-33(2)11-13-34/h4-9,14-15,17H,1,10-13,16H2,2-3H3,(H,30,35)(H2,28,29,31,32)
Release date: 2016-02-10
Binary complex of DNA Polymerase Beta with Ring open Intermediate Fapy-dG in the template position (PDB entry 7S9O)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.23
R work: 0.2015
R free: 0.2777
Average B factor: 35.54
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
Matthews coefficient: 2.35
Solvent content (%): 47.75
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2022-08-03
Crystal Structure of human phosphodiesterase 10 in complex with 2-methyl-3-[(1-methyl-4-phenylimidazol-2-yl)methoxy]quinoxaline (PDB entry 5SF9)
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): 2.37
R work: 0.175
R free: 0.2293
Average B factor: 56.097
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 (%): 53.57
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 Cyclophilin D Complexed with Inhibitor (PDB entry 5CCQ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.16381
R free: 0.2027
Average B factor: 16.281
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9
Crystallization temperature (K): 294
Crystal growth procedure: 4M potassium formate, 0.1M BIS-TRIS propane pH 9, 2% w/v PEG2000mme
Matthews coefficient: 2.66
Solvent content (%): 53.79
Ligand: FORMIC ACID (FMT)
Ligand formula: C H2 O2
Ligand molecular weight: 46.025
Ligand SMILES: C(=O)O
Ligand InChI: InChI=1S/CH2O2/c2-1-3/h1H,(H,2,3)
Release date: 2016-07-20
Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.1 A resolution (PDB entry 6JB7)
Macromolecule: Ubiquitin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 76 residues
Sequence: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.2148
R free: 0.2503
Average B factor: 29.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: HEPES, PEG 400, magnesium chloride
Matthews coefficient: 2.56
Solvent content (%): 54.59
Release date: 2019-03-20
EGFR kinase domain mutant "TMLR" with compound 41a (PDB entry 5CAS)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 331 residues
Sequence: GSGEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLIMQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGRAKLLGAAAAEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQGNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.1825
R free: 0.2091
Average B factor: 60.42
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 292
Crystal growth procedure: PEG 10000, ethylene glycol
Matthews coefficient: 3.46
Solvent content (%): 64.47
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2015-10-28
Crystal structure of HIV-1 reverse transcriptase with a double stranded DNA showing a transient P-pocket (PDB entry 7OZ2)
Macromolecule: Reverse transcriptase/ribonuclease H
Type: Protein, polypeptide(L)
Source organism: Human immunodeficiency virus type 1 BH10
EC number: 2.7.7.49
Sequence length: 556 residues
Sequence: MVPISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFACKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWETWWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNKGRQKVVPLTNTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDKSESELVNQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDKLVSA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.85
R work: 0.217
R free: 0.257
Average B factor: 63.18
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 11-12% v/v PEG Smear Broad, 10% w/v sucrose, 50 mM PIPES-NaOH pH 6.5, 0.1 M (NH4)2SO4, 5 mM MgCl2, 5 mM CdCl2
Matthews coefficient: 3.04
Solvent content (%): 59.6
Ligand: CADMIUM ION (CD)
Ligand formula: Cd
Ligand molecular weight: 112.411
Ligand SMILES: [Cd+2]
Ligand InChI: InChI=1S/Cd/q+2
Release date: 2021-12-08
Structure of the MDM2 P53 binding domain in complex with H101, an all-D Helicon Polypeptide (PDB entry 8F0Z)
Macromolecule: E3 ubiquitin-protein ligase Mdm2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 95 residues
Sequence: SQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHRKIYTMIYRNLVVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.61
R work: 0.2209
R free: 0.2423
Average B factor: 35.5855
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 3.5 M Sodium Formate pH 7.0
Matthews coefficient: 2.22
Solvent content (%): 44.59
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2023-02-15
Crystal structure of human NRMT2 in complex with human centromere protein B peptide (PDB entry 6KDR)
Macromolecule: Alpha N-terminal protein methyltransferase 1B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.299
Sequence length: 244 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMVINGEMQFYARAKLFYQEVPATEEGMMGNFIELSSPDIQASQKFLRKFVGGPGRAGTDCALDCGSGIGRVSKHVLLPVFNSVELVDMMESFLLEAQNYLQVKGDKVESYHCYSLQEFTPPFRRYDVIWIQWVSGHLTDKDLLAFLSRCRDGLKENGIIILKDNVAREGCILDLSDSSVTRDMDILRSLIRKSGLVVLGQEKQDGFPEQCIPVWMFALHSDRHS
Oligomeric state: Hetero 4-mer
Stoichiometry: A2, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.112
R work: 0.1783
R free: 0.2047
Average B factor: 43.636
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.3
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M Tris pH 8.3, 6% w/v Polyethylene glycol 8000
Matthews coefficient: 2.98
Solvent content (%): 58.73
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2020-07-08
Carbonic Anhydrase IX mimic complexed with 4-(2-(3-(4-fluorophenyl)ureido)ethylsulfonamido)benzenesulfonamide (PDB entry 7K6Z)
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): 1.657
R work: 0.1837
R free: 0.2119
Average B factor: 21.3857
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.4
Crystallization temperature (K): 295
Crystal growth procedure: 1.6M Sodium Citrate, 50mM Tris, pH 6.4
Matthews coefficient: 2.13
Solvent content (%): 42.14
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-12-23
Crystal structure for the complex of human carbonic anhydrase II and 3-(3-methyl-3-phenethylureido)benzenesulfonamide (PDB entry 7ASJ)
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): 1.43
R work: 0.1487
R free: 0.1791
Average B factor: 15.516
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 1.5 M sodium citrate, Tris 50 mM
Matthews coefficient: 2.09
Solvent content (%): 41.03
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: 2021-11-24
Crystal structure of D1228V c-MET bound by compound 2 (PDB entry 8OWG)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 309 residues
Sequence: GDSDISSPLLQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARVMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.631
R work: 0.2806
R free: 0.3292
Average B factor: 41.58
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 15 % PEG2000 MME, 0.1 M PCPT pH 6.5
Matthews coefficient: 2.28
Solvent content (%): 46.13
Ligand: 5-[3,5-bis(fluoranyl)phenyl]-1-[(1S)-1-phenylethyl]pyrimidine-2,4-dione (W40)
Ligand formula: C18 H14 F2 N2 O2
Ligand molecular weight: 328.313
Ligand SMILES: CC(c1ccccc1)N2C=C(C(=O)NC2=O)c3cc(cc(c3)F)F
Ligand InChI: InChI=1S/C18H14F2N2O2/c1-11(12-5-3-2-4-6-12)22-10-16(17(23)21-18(22)24)13-7-14(19)9-15(20)8-13/h2-11H,1H3,(H,21,23,24)/t11-/m0/s1
Release date: 2023-07-05
Structure of the MOB1-NDR2 complex (PDB entry 5XQZ)
Macromolecule: MOB kinase activator 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 193 residues
Sequence: AAHHSSGHMEATLGSGNLRQAVMLPEGEDLNEWIAVNTVDFFNQINMLYGTITEFCTEASCPVMSAGPRYEYHWADGTNIKKPIKCSAPKYIDYLMTWVQDQLDDETLFPSKIGVPFPKNFMSVAKTILKRLFRVYAHIYHQHFDSVMQLQEEAHLNTSFKHFIFFVQEFNLIDRRELAPLQELIEKLGSKDR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.15631
R free: 0.24374
Average B factor: 36.202
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 287
Crystal growth procedure: PEG 3350, HEPES, magnesium chloride
Matthews coefficient: 2.34
Solvent content (%): 47.4
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: 2018-08-29
CRYSTAL STRUCTURE OF HUMAN G3BP1-NTF2 IN COMPLEX WITH HUMAN CAPRIN1-DERIVED SOLOMON MOTIF (PDB entry 6TA7)
Macromolecule: Ras GTPase-activating protein-binding protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.12
Sequence length: 140 residues
Sequence: SMVMEKPSPLLVGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNFTNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRRFMQTFVLAPEGSVANKFYVHNDIFRYQDEVFG
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.2067
R free: 0.2518
Average B factor: 60.84
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.2M Sodium chloride, 0.1M Tris 8.0, 20% w/v PEG 4000 of the Proplex crystallization screen (Molecular Dimensions)
Matthews coefficient: 2.24
Solvent content (%): 45
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2021-05-12
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3,6-Dihydroxybenzonorbornane (N08776b) (ligand modelled based on PANDDA event map) (PDB entry 5FZ3)
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): 2.5
R work: 0.171
R free: 0.2171
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: 2.17
Solvent content (%): 43.3
Ligand: (1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalene-5,8-diol (7SI)
Ligand formula: C11 H12 O2
Ligand molecular weight: 176.212
Ligand SMILES: c1cc(c2c(c1O)C3CCC2C3)O
Ligand InChI: InChI=1S/C11H12O2/c12-8-3-4-9(13)11-7-2-1-6(5-7)10(8)11/h3-4,6-7,12-13H,1-2,5H2/t6-,7+
Release date: 2016-03-23
PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with Z2895259680 (PDB entry 5QOQ)
Macromolecule: DCP2 (NUDT20)
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.62
Sequence length: 167 residues
Sequence: SMGVPTYGAIILDETLENVLLVQGYLAKSGWGFPKGKVNKEEAPHDCAAREVFEETGFDIKDYICKDDYIELRINDQLARLYIIPGIPKDTKFNPKTRREIRNIEWFSIEKLPCHRNDMTPKSKLGLAPNKFFMAIPFIRPLRDWLSRRFGDSSDSDNGFSSTGSTP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.2116
R free: 0.2567
Average B factor: 32.344
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M acetate, pH 4.5, 5-25% PEG3350
Matthews coefficient: 2.52
Solvent content (%): 51.13
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2019-05-08
Human APE1 C65A AP-endonuclease product complex (PDB entry 6P94)
Macromolecule: DNA-(apurinic or apyrimidinic site) lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1
Sequence length: 276 residues
Sequence: ALYEDPPDQKTSPSGKPATLKIASWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.09
R work: 0.1862
R free: 0.2445
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 10% PEG20000, 100 mM sodium citrate, pH 5.0, and 200 mM MgCl2
Matthews coefficient: 2.47
Solvent content (%): 50.16
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: 2020-01-01
Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 10 mM Mn2+ for 600s (PDB entry 5KFQ)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1918
R free: 0.223
Average B factor: 32.733
Crystallization method: EVAPORATION
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 17% PEG 2000MME, 0.1 M MES
Matthews coefficient: 2.09
Solvent content (%): 41.1
Ligand: MANGANESE (II) ION (MN)
Ligand formula: Mn
Ligand molecular weight: 54.938
Ligand SMILES: [Mn+2]
Ligand InChI: InChI=1S/Mn/q+2
Release date: 2016-06-29
Crystal structure of JAK3 kinase domain in complex with a pyrrolopyridazine carboxamide inhibitor (PDB entry 6NY4)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 293 residues
Sequence: GPASQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.33
R work: 0.215
R free: 0.241
Average B factor: 56.28
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.8
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG3350, 200 mM magnesium chloride, 100 mM Bis-Tris, pH 5.8
Matthews coefficient: 2.37
Solvent content (%): 48.15
Ligand: 4-{[(2R,3R)-1,3-dihydroxybutan-2-yl]amino}-6-phenylpyrrolo[1,2-b]pyridazine-3-carboxamide (Z3A)
Ligand formula: C18 H20 N4 O3
Ligand molecular weight: 340.376
Ligand SMILES: CC(C(CO)Nc1c2cc(cn2ncc1C(=O)N)c3ccccc3)O
Ligand InChI: InChI=1S/C18H20N4O3/c1-11(24)15(10-23)21-17-14(18(19)25)8-20-22-9-13(7-16(17)22)12-5-3-2-4-6-12/h2-9,11,15,21,23-24H,10H2,1H3,(H2,19,25)/t11-,15-/m1/s1
Release date: 2019-05-22