satarupa22/MacromolecularLigandDB huggingface dataset:
hMiro1 C-domain GDP Complex C2221 Crystal Form (PDB entry 5KSP)
Macromolecule: Mitochondrial Rho GTPase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5
Sequence length: 190 residues
Sequence: KKQTQRNVFRCNVIGVKNCGKSGVLQALLGRNLMRQKKIREDHKSYYAINTVYVYGQEKYLLLHDISESEFLTEAEIICDVVCLVYDVSNPKSFEYCARIFKQHFMDSRIPCLIVAAKSDLHEVKQEYSISPTDFCRKHKMPPPQAFTCNTADAPSKDIFVKLTTMAMYPHVTQADLKSSTFLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.162
R work: 0.1929
R free: 0.2412
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 294
Crystal growth procedure: 15 mg/mL protein, 6 mM magnesium chloride, 0.1 M Tris, pH 8.5, 12% w/v PEG4000, GDP observed in the structure was carried through from the expression system during purification
Matthews coefficient: 2.07
Solvent content (%): 40.6
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: 2016-09-21
Crystal Structure of human phosphodiesterase 10 in complex with 5-(cyclopentylmethoxy)pyrimidin-2-amine (PDB entry 5SIK)
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): 2.1
R work: 0.183
R free: 0.2224
Average B factor: 46.049
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: 2.6
Solvent content (%): 52.63
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
Crystal structure of ZAK in complex with compound YH-186 (PDB entry 7YAZ)
Macromolecule: Mitogen-activated protein kinase kinase kinase MLT
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 310 residues
Sequence: GAMGSGASFVQIKFDDLQFFENCGGGSFGSVYRAKWISQDKEVAVKKLLKIEKEAEILSVLSHRNIIQFYGVILEPPNYGIVTEYASLGSLYDYINSNRSEEMDMDHIMTWATDVAKGMHYLHMEAPVKVIHRDLKSRNVVIAADGVLKICDFGASRFHNHTTHMSLVGTFPWMAPEVIQSLPVSETCDTYSYGVVLWEMLTREVPFKGLEGLQVAWLVVEKNERLTIPSSCPRSFAELLHQCWEADAKKRPSFKQIISILESMSNDTSLPDKCNSFLHNKAEWRCEIEATLERLKKLERDLSFKEQELK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.1835
R free: 0.2518
Average B factor: 42.8447
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.05 M Magnesium acetate, 0.05 M Sodium acetate pH 5.0, 28% PEG400
Matthews coefficient: 1.84
Solvent content (%): 33.31
Ligand: ~{N}-[2,4-bis(fluoranyl)-3-[4-[3-[(3~{S})-1-propanoylpyrrolidin-3-yl]oxy-1~{H}-pyrazolo[3,4-b]pyridin-5-yl]-1,2,3-triazol-1-yl]phenyl]-3-phenyl-benzenesulfonamide (IGV)
Ligand formula: C33 H28 F2 N8 O4 S
Ligand molecular weight: 670.688
Ligand SMILES: CCC(=O)N1CCC(C1)Oc2c3cc(cnc3[nH]n2)c4cn(nn4)c5c(ccc(c5F)NS(=O)(=O)c6cccc(c6)c7ccccc7)F
Ligand InChI: InChI=1S/C33H28F2N8O4S/c1-2-29(44)42-14-13-23(18-42)47-33-25-16-22(17-36-32(25)38-39-33)28-19-43(41-37-28)31-26(34)11-12-27(30(31)35)40-48(45,46)24-10-6-9-21(15-24)20-7-4-3-5-8-20/h3-12,15-17,19,23,40H,2,13-14,18H2,1H3,(H,36,38,39)/t23-/m0/s1
Release date: 2023-08-09
Crystal Structure of human phosphodiesterase 10 in complex with 3-[2-(3-bromophenyl)pyrazol-3-yl]-1-pyridin-4-ylpyridazin-4-one (PDB entry 5SHB)
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): 1.95
R work: 0.1805
R free: 0.2149
Average B factor: 34.323
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: 2.63
Solvent content (%): 53.32
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
Crystal structure of human cathepsin D in complex with macrocyclic inhibitor 14 (PDB entry 6QBG)
Macromolecule: Cathepsin D
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.5
Sequence length: 98 residues
Sequence: GPIPEVLKNYMDAQYYGEIGIGTPPQCFTVVFDTGSSNLWVPSIHCKLLDIACWIHHKYNSDKSSTYVKNGTSFDIHYGSGSLSGYLSQDTVSVPCQS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1941
R free: 0.247
Average B factor: 29.169
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 25% PEG 3350
0.2 M lithium sulphate 
0.1 M Bis-Tris pH 5.5
Matthews coefficient: 2.99
Solvent content (%): 58.91
Ligand: (3~{S},7~{S},8~{S})-8-(naphthalen-2-ylmethyl)-7-oxidanyl-3-propan-2-yl-1,4,9-triazacyclohenicosane-2,5,10-trione (HVT)
Ligand formula: C32 H47 N3 O4
Ligand molecular weight: 537.733
Ligand SMILES: CC(C)C1C(=O)NCCCCCCCCCCCC(=O)NC(C(CC(=O)N1)O)Cc2ccc3ccccc3c2
Ligand InChI: InChI=1S/C32H47N3O4/c1-23(2)31-32(39)33-19-13-9-7-5-3-4-6-8-10-16-29(37)34-27(28(36)22-30(38)35-31)21-24-17-18-25-14-11-12-15-26(25)20-24/h11-12,14-15,17-18,20,23,27-28,31,36H,3-10,13,16,19,21-22H2,1-2H3,(H,33,39)(H,34,37)(H,35,38)/t27-,28-,31-/m0/s1
Release date: 2020-01-29
Jak3 with covalent inhibitor 4 (PDB entry 5TTS)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 321 residues
Sequence: MGHHHHHHQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGCERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWSGSRGCETHAFTAHPEGKHHSLSFS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.34
R work: 0.2022
R free: 0.2633
Average B factor: 47.46
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG 3350, 0.2M (NH4)2SO4, 2% phenylurea
Matthews coefficient: 2.2
Solvent content (%): 44.05
Ligand: 1-{(3R)-3-[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}propan-1-one (7KU)
Ligand formula: C14 H19 N5 O
Ligand molecular weight: 273.334
Ligand SMILES: CCC(=O)N1CCCC(C1)Nc2c3cc[nH]c3ncn2
Ligand InChI: InChI=1S/C14H19N5O/c1-2-12(20)19-7-3-4-10(8-19)18-14-11-5-6-15-13(11)16-9-17-14/h5-6,9-10H,2-4,7-8H2,1H3,(H2,15,16,17,18)/t10-/m1/s1
Release date: 2017-02-22
Crystal structure of JAK1 in complex with peficitinib (PDB entry 6AAH)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 290 residues
Sequence: VDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.83
R work: 0.22374
R free: 0.25502
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: buffer, salt, precipitant
Matthews coefficient: 2.31
Solvent content (%): 46.74
Ligand: 4-[[(1S,3R)-5-oxidanyl-2-adamantyl]amino]-1H-pyrrolo[2,3-b]pyridine-5-carboxamide (9T6)
Ligand formula: C18 H22 N4 O2
Ligand molecular weight: 326.393
Ligand SMILES: c1c[nH]c2c1c(c(cn2)C(=O)N)NC3C4CC5CC3CC(C5)(C4)O
Ligand InChI: InChI=1S/C18H22N4O2/c19-16(23)13-8-21-17-12(1-2-20-17)15(13)22-14-10-3-9-4-11(14)7-18(24,5-9)6-10/h1-2,8-11,14,24H,3-7H2,(H2,19,23)(H2,20,21,22)/t9-,10-,11+,14-,18-
Release date: 2018-08-15
TTK kinase domain in complex with MPI-0479605 (PDB entry 5N7V)
Macromolecule: Dual specificity protein kinase TTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.1
Sequence length: 313 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHLVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.52
R work: 0.19442
R free: 0.27839
Average B factor: 88.663
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.3
Crystallization temperature (K): 273
Crystal growth procedure: 32 - 37% PEG400 (Acros, Geel, Belgium), 0.1 M Na/K phosphate pH 6.3 and 250 mM NaCl
Matthews coefficient: 3.14
Solvent content (%): 60.82
Ligand: ~{N}6-cyclohexyl-~{N}2-(2-methyl-4-morpholin-4-yl-phenyl)-7~{H}-purine-2,6-diamine (8PT)
Ligand formula: C22 H29 N7 O
Ligand molecular weight: 407.512
Ligand SMILES: Cc1cc(ccc1Nc2nc3c(c(n2)NC4CCCCC4)[nH]cn3)N5CCOCC5
Ligand InChI: InChI=1S/C22H29N7O/c1-15-13-17(29-9-11-30-12-10-29)7-8-18(15)26-22-27-20-19(23-14-24-20)21(28-22)25-16-5-3-2-4-6-16/h7-8,13-14,16H,2-6,9-12H2,1H3,(H3,23,24,25,26,27,28)
Release date: 2017-05-31
Crystal structure of PTP1B D181A/Q262A/C215A phosphatase domain with a JAK2 activation loop phosphopeptide (PDB entry 8EYA)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 302 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPAFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHASAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIATADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.099
R work: 0.2206
R free: 0.2604
Average B factor: 50.3722
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281.15
Crystal growth procedure: 25% w/v PEG 3350, 0.2 M NaCl, 0.1 M Tris Cl (pH 8.5)
Matthews coefficient: 3.14
Solvent content (%): 60.83
Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS)
Ligand formula: C4 H12 N O3
Ligand molecular weight: 122.143
Ligand SMILES: C(C(CO)(CO)[NH3+])O
Ligand InChI: InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1
Release date: 2023-07-05
Crystal structure of human BIRC2 BIR3 domain in complex with histone H3 (PDB entry 7TRL)
Macromolecule: Baculoviral IAP repeat-containing protein 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.2.27
Sequence length: 94 residues
Sequence: GPLGSPEFISNLSMQTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIRMKGQEFVD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.1623
R free: 0.206
Average B factor: 22.72
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M SPG buffer (2:7:7 molar ratio of succinic acid:sodium dihydrogen phosphate: glycine), 25% PEG 1,500
Matthews coefficient: 1.68
Solvent content (%): 26.63
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2023-08-02
Peptide GNYKEAKK in complex with human cathepsin V C25A mutant (PDB entry 7Q8F)
Macromolecule: Cathepsin L2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.43
Sequence length: 221 residues
Sequence: LPKSVDWRKKGYVTPVKNQKQCGSAWAFSATGALEGQMFRKTGKLVSLSEQNLVDCSRPQGNQGCNGGFMARAFQYVKENGGLDSEESYPYVAVDEICKYRPENSVAQDTGFTVVAPGKEKALMKAVATVGPISVAMDAGHSSFQFYKSGIYFEPDCSSKNLDHGVLVVGYGFEGANSQNSKYWLVKNSWGPEWGSNGYVKIAKDKNNHCGIATAASYPNV
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.49
R work: 0.175
R free: 0.1969
Average B factor: 28.62
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 77 % MPD, 23 % of Tris, pH 8
Matthews coefficient: 2.79
Solvent content (%): 55.99
Ligand: (4S)-2-METHYL-2,4-PENTANEDIOL (MPD)
Ligand formula: C6 H14 O2
Ligand molecular weight: 118.174
Ligand SMILES: CC(CC(C)(C)O)O
Ligand InChI: InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
Release date: 2022-11-23
Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor edaGDP (PDB entry 7OK3)
Macromolecule: Isoform 2B of GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: HMTEYKLVVVGAGCVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETSLLDILDTAGQEEYSAMRDQYMRTGEGFLLVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKSDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.158
R free: 0.2001
Average B factor: 27.867
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.2 M (NH4)F, 20 % PEG3350, 67 mg/mL KRasG13C-edaGDP, 0.1 uL reservoir + 0.1 uL protein solution
Matthews coefficient: 2.17
Solvent content (%): 43.29
Ligand: edaGDP (VJ8)
Ligand formula: C16 H25 N7 O13 P2
Ligand molecular weight: 585.356
Ligand SMILES: CCC(=O)NCCNC(=O)OC1C(OC(C1O)n2cnc3c2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)O
Ligand InChI: InChI=1S/C16H25N7O13P2/c1-2-8(24)18-3-4-19-16(27)35-11-7(5-33-38(31,32)36-37(28,29)30)34-14(10(11)25)23-6-20-9-12(23)21-15(17)22-13(9)26/h6-7,10-11,14,25H,2-5H2,1H3,(H,18,24)(H,19,27)(H,31,32)(H2,28,29,30)(H3,17,21,22,26)/t7-,10-,11-,14-/m1/s1
Release date: 2022-08-03
PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid) (PDB entry 5NP8)
Macromolecule: Phosphoglycerate kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.2.3
Sequence length: 420 residues
Sequence: GSHMSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGVPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKVKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.16792
R free: 0.22183
Average B factor: 24.778
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 2.4-2.8M Sodium potassium phosphate, pH 7.4 - 8.2, 10mM DTT
Matthews coefficient: 2.07
Solvent content (%): 40.67
Ligand: 3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid (93T)
Ligand formula: C17 H16 Br N3 O2
Ligand molecular weight: 374.232
Ligand SMILES: Cc1c(c(n2c(n1)cc(n2)c3ccc(cc3)Br)C)CCC(=O)O
Ligand InChI: InChI=1S/C17H16BrN3O2/c1-10-14(7-8-17(22)23)11(2)21-16(19-10)9-15(20-21)12-3-5-13(18)6-4-12/h3-6,9H,7-8H2,1-2H3,(H,22,23)
Release date: 2018-05-16
Human PI3Kdelta in complex with Compound 4-2 ((3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one) (PDB entry 6PYU)
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: 1018 residues
Sequence: NQSVVVDFLLPTGVYLNFPVSRNANLSTIKQLLWHRAQYEPLFHMLSGPEAYVFTCINQTAEQQELEDEQRRLCDVQPFLPVLRLVAREGDRVKKLINSQISLLIGKGLHEFDSLCDPEVNDFRAKMCQFCEEAAARRQQLGWEAWLQYSFPLQLEPSAQTWGPGTLRLPNRALLVNVKFEGSEESFTFQVSTKDVPLALMACALRKKATVFRQPLVEQPEDYTLQVNGRHEYLYGSYPLCQFQYICSCLHSGLTPHLTMVHSSSILAMRDEQSNPAPQVQKPRAKPPPIPAKKPSSVSLWSLEQPFRIELIQGSKVNADERMKLVVQAGLFHGNEMLCKTVSSSEVSVCSEPVWKQRLEFDINICDLPRMARLCFALYAVIEKAKKARSTKKKSKKADCPIAWANLMLFDYKDQLKTGERCLYMWPSVPDEKGELLNPTGTVRSNPNTDSAAALLICLPEVAPHPVYYPALEKILELGRHSECVHVTEEEQLQLREILERRGSGELYEHEKDLVWKLRHEVQEHFPEALARLLLVTKWNKHEDVAQMLYLLCSWPELPVLSALELLDFSFPDCHVGSFAIKSLRKLTDDELFQYLLQLVQVLKYESYLDCELTKFLLDRALANRKIGHFLFWHLRSEMHVPSVALRFGLILEAYCRGSTHHMKVLMKQGEALSKLKALNDFVKLSSQKTPKPQTKELMHLCMRQEAYLEALSHLQSPLDPSTLLAEVCVEQCTFMDSKMKPLWIMYSNEEAGSGGSVGIIFKNGDDLRQDMLTLQMIQLMDVLWKQEGLDLRMTPYGCLPTGDRTGLIEVVLRSDTIANIQLNKSNMAATAAFNKDALLNWLKSKNPGEALDRAIEEFTLSCAGYCVATYVLGIGDRHSDNIMIRESGQLFHIDFGHFLGNFKTKFGINRERVPFILTYDFVHVIQQGKTNNSEKFERFRGYCERAYTILRRHGLLFLHLFALMRAAGLPELSCSKDIQYLKDSLALGKTEEEALKHFRVKFNEALRESWKTKVNWL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.54
R work: 0.2397
R free: 0.2916
Average B factor: 106.112
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: not available
Matthews coefficient: 2.63
Solvent content (%): 53.19
Ligand: (3S)-1'-(cyclopropanecarbonyl)-5-(quinoxalin-6-yl)spiro[indole-3,2'-pyrrolidin]-2(1H)-one (P5V)
Ligand formula: C23 H20 N4 O2
Ligand molecular weight: 384.431
Ligand SMILES: c1cc2c(cc1c3ccc4c(c3)C5(CCCN5C(=O)C6CC6)C(=O)N4)nccn2
Ligand InChI: InChI=1S/C23H20N4O2/c28-21(14-2-3-14)27-11-1-8-23(27)17-12-15(4-6-18(17)26-22(23)29)16-5-7-19-20(13-16)25-10-9-24-19/h4-7,9-10,12-14H,1-3,8,11H2,(H,26,29)/t23-/m0/s1
Release date: 2019-08-28
SYK kinase domain in complex with inhibitor GTC000225 (PDB entry 4YJR)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 281 residues
Sequence: PEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.32
R work: 0.1555
R free: 0.1801
Average B factor: 18.53
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 293
Crystal growth procedure: 30% Jeffamine ED-2001, 10% Glycerol, 0.1M MES pH6.0, 5mM TCEP
Matthews coefficient: 2.1
Solvent content (%): 41.5
Ligand: 3-(1H-indazol-4-yl{2-[(1-methyl-1H-indazol-5-yl)amino]pyrimidin-4-yl}amino)propan-1-ol (4DJ)
Ligand formula: C22 H22 N8 O
Ligand molecular weight: 414.463
Ligand SMILES: Cn1c2ccc(cc2cn1)Nc3nccc(n3)N(CCCO)c4cccc5c4cn[nH]5
Ligand InChI: InChI=1S/C22H22N8O/c1-29-19-7-6-16(12-15(19)13-25-29)26-22-23-9-8-21(27-22)30(10-3-11-31)20-5-2-4-18-17(20)14-24-28-18/h2,4-9,12-14,31H,3,10-11H2,1H3,(H,24,28)(H,23,26,27)
Release date: 2015-09-30
Factor XIa in complex with the inhibitor methyl (4-{4-chloro-2-[(1S)-1-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-3-(morpholin-4-yl)-3-oxopropyl]-1H-imidazol-5-yl}phenyl)carbamate (PDB entry 4Y8Y)
Macromolecule: Coagulation factor XIa
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.27
Sequence length: 244 residues
Sequence: IVGGTASVRGEWPWQVTLHTTSPTQRHLCGGSIIGNQWILTAAHCFYGVESPKILRVYSGILNQSEIKEDTSFFGVQEIIIHDQYKMAESGYDIALLKLETTVGYGDSQRPICLPSKGDRNVIYTDCWVTGWGYRKLRDKIQNTLQKAKIPLVTNEECQKRYRGHKITHKMICAGYREGGKDACKGDSGGPLSCKHNEVWHLVGITSWGEGCAQRERPGVYTNVVEYVDWILEKTQAVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.1961
R free: 0.2406
Average B factor: 23.33
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM sodium acetate, pH 4.6, 26% w/v MEPEG2000, 200 mM ammonium sulfate
Matthews coefficient: 3.58
Solvent content (%): 65.69
Ligand: methyl (4-{4-chloro-2-[(1S)-1-({(2E)-3-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]prop-2-enoyl}amino)-3-(morpholin-4-yl)-3-oxopropyl]-1H-imidazol-5-yl}phenyl)carbamate (4D5)
Ligand formula: C28 H27 Cl2 N9 O5
Ligand molecular weight: 640.477
Ligand SMILES: COC(=O)Nc1ccc(cc1)c2c(nc([nH]2)C(CC(=O)N3CCOCC3)NC(=O)C=Cc4cc(ccc4n5cnnn5)Cl)Cl
Ligand InChI: InChI=1S/C28H27Cl2N9O5/c1-43-28(42)32-20-6-2-17(3-7-20)25-26(30)35-27(34-25)21(15-24(41)38-10-12-44-13-11-38)33-23(40)9-4-18-14-19(29)5-8-22(18)39-16-31-36-37-39/h2-9,14,16,21H,10-13,15H2,1H3,(H,32,42)(H,33,40)(H,34,35)/b9-4+/t21-/m0/s1
Release date: 2015-05-27
Crystal structure of PIM1 with inhibitor: 3-(4-methoxyphenyl)-1~{H}-pyrazol-5-amine (PDB entry 5KGK)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 276 residues
Sequence: EKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.66
R work: 0.187
R free: 0.206
Average B factor: 64.01
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 293
Crystal growth procedure: 18% PEG 3350, 0.2 M Na2SO4, 6% ethylene glycol, 0.1 M Tris, pH 7.3
Matthews coefficient: 3.58
Solvent content (%): 65.62
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2017-08-09