satarupa22/MacromolecularLigandDB huggingface dataset:
STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE BISUBSTRATE INHIBITOR ARC-780 (PDB entry 8Q77)
Macromolecule: Casein kinase II subunit alpha'
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: MGSSHHHHHHSQDPMPGPAAGSRARVYAEVNSLRSREYWDYEAHVPSWGNQDDYQLVRKLGRGKYSEVFEAINITNNERVVVKILKPVKKKKIKREVKILENLRGGTNIIKLIDTVKDPVSKTPALVFEYINNTDFKQLYQILTDFDIRFYMYELLKALDYCHSKGIMHRDVKPHNVMIDHQQKKLRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRREPFFHGQDNYDQLVRIAKVLGTEELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQQRLTAKEAMEHPYFYPVVKEQSQPSADNAVLSSGLTAAR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.255
R work: 0.1197
R free: 0.157
Average B factor: 16.47
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: THE CK2ALPHA' SOLUTION AFTER PROTEIN PURIFICATION (5 MG/ML CK2ALPHA' IN 500 MM NACL, 25 MM TRIS/HCl, PH 8.5) WAS MIXED IN 1:10 VOLUME RATIO WITH 10 MM SOLUTION OF THE INHIBITOR MB002 IN DMSO. THIS SOLUTION WAS MIXED IN 2:1 RATIO WITH RESERVOIR SOLUTION [900 MM LICL, 28 % (W/V) PEG 6000, 250 MM TRIS/HCL, PH 8.5] IN SITTING DROP PLATES (VAPOUR DIFFUSION). THE CRYSTAL GROWTH WAS INDUCED BY MICROSEEDING. THE CRYSTALS WERE OPTIMIZED BY MACROSEEDING AND PURGED TWICE WITH RESERVOIR SOLUTION. THEN, ARC-780 WAS ADDED TO AN INITIAL CONCENTRATION OF 1 MM BY ADDING 1 MIKROLITER OF A 10 MM ARC-780 SOLUTION IN DMSO IN A 1:10 RATIO TO THE DROPLET. AFTER EXTENSIVE INTIAL SOAKING, THE SALT CONCENTRATION WAS SUCCESSIVELY LOWERED OVER A PERIOD OF 8 MONTHS WHILE IN PARALLEL THE CONCENTRATIONS OF DMSO AND PEG 6000 WERE INCREASED. THIS WAS DONE BY GRADUALLY REPLACING THE RESERVOIR AND THE DROPLET SOLUTION UNTIL ANY NACL WAS REMOVED, THE LICL CONCENTRATION WAS REDUCED TO 50 MM, THE PEG 6000 CONCENTRATION WAS INCREASED TO SATURATION AND A DMSO CONTENT OF 30% WAS REACHED. MEANWHILE, THE ARC-780 LIGAND WAS INCLUDED IN ANY DESALTING STEP REACHING SATURATION AFTER THE FINAL DILUTION STEP. ALL STEPS WERE PERFORMED AT A TEMPERATURE OF 293 K.
Matthews coefficient: 2.66
Solvent content (%): 53.84
Ligand: (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[12-[[4-[[5-(4-carboxyphenyl)-1,3-thiazol-2-yl]amino]-4-oxidanylidene-butanoyl]-(2-hydroxy-2-oxoethyl)amino]dodecanoylamino]-4-oxidanyl-4-oxidanylidene-butanoyl]amino]-4-oxidanyl-4-oxidanylidene-butanoyl]amino]butanedioic acid (LN3)
Ligand formula: C40 H52 N6 O17 S
Ligand molecular weight: 920.936
Ligand SMILES: c1cc(ccc1c2cnc(s2)NC(=O)CCC(=O)N(CCCCCCCCCCCC(=O)NC(CC(=O)O)C(=O)NC(CC(=O)O)C(=O)NC(CC(=O)O)C(=O)O)CC(=O)O)C(=O)O
Ligand InChI: InChI=1S/C40H52N6O17S/c47-29(42-25(18-32(50)51)36(58)43-26(19-33(52)53)37(59)44-27(39(62)63)20-34(54)55)10-8-6-4-2-1-3-5-7-9-17-46(22-35(56)57)31(49)16-15-30(48)45-40-41-21-28(64-40)23-11-13-24(14-12-23)38(60)61/h11-14,21,25-27H,1-10,15-20,22H2,(H,42,47)(H,43,58)(H,44,59)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,60,61)(H,62,63)(H,41,45,48)/t25-,26-,27-/m0/s1
Release date: 2023-12-06
Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and allosteric binding modes (PDB entry 6YG2)
Macromolecule: Dual specificity mitogen-activated protein kinase kinase 7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.12.2
Sequence length: 307 residues
Sequence: SMKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1789
R free: 0.2304
Average B factor: 38.529
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 277.15
Crystal growth procedure: 19% PEG3350, 
0.1 M ammonium acetate,
0.1 M tris, pH 7.8
Matthews coefficient: 2.47
Solvent content (%): 50.17
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: 2020-08-12
Crystal Structure of human phosphodiesterase 10 in complex with 6-cyclopropyl-N-[2-(2-hydroxyethyl)-5-pyridin-2-ylpyrazol-3-yl]-3-(pyrimidin-5-ylamino)pyridine-2-carboxamide (PDB entry 5SE0)
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): 2.01
R work: 0.1932
R free: 0.2264
Average B factor: 36.822
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 (%): 53.51
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
Naturally Occurring Mutations in the MPS1 Gene Predispose Cells to Kinase Inhibitor Drug Resistance. (PDB entry 5AP5)
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: MHHHHHHSSGVDLGTENLYFQSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNGWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQTHPVNQMAKGTTEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2027
R free: 0.2457
Average B factor: 101.63
Crystallization pH: 7.5
Crystal growth procedure: 38% (V/V) PEG300, PH 7.5
Matthews coefficient: 3.09
Solvent content (%): 60.23
Ligand: TRIETHYLENE GLYCOL (PGE)
Ligand formula: C6 H14 O4
Ligand molecular weight: 150.173
Ligand SMILES: C(COCCOCCO)O
Ligand InChI: InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2
Release date: 2015-09-23
Crystal structure of FGFR2 in complex with 1,3,5-triazine derivative (PDB entry 6LVL)
Macromolecule: Fibroblast growth factor receptor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 313 residues
Sequence: GSHMLAGVSEYELPEDPKWEFPRDKLTLGKPLGEGCFGQVVMAEAVGIDKDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLRARRPPGMEYSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIHRDLAARNVLVTENNVMKIADFGLARDINNIDYYKKTTNGRLPVKWMAPEALFDRVYTHQSDVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRILTLTTNEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.98
R work: 0.2019
R free: 0.2506
Average B factor: 26.484
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 296
Crystal growth procedure: Tris, Ammonium sulfate, PEG 8000
Matthews coefficient: 2.75
Solvent content (%): 55.28
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: 2020-04-08
Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with AZD-7762 (PDB entry 7CQE)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 294 residues
Sequence: EELQNKLEDVVIDRNLLILGKILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPKHIPLQTLLKFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLEKLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.1968
R free: 0.2593
Average B factor: 38.415
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 287
Crystal growth procedure: Protein 40mg/mL in 20mM Tris-Cl, pH 8.0, 500mM sodium chloride, 2mM DTT. inhibitor (5 mM final concentration) overnight, Mixed 1:1 with crystallization solution (100mM Tris-Cl, pH 8.5, 4M sodium chloride)
Matthews coefficient: 2.42
Solvent content (%): 49.19
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: 2020-11-04
The crystal structure of humanMGME1 with single strand DNA2 (PDB entry 5ZYU)
Macromolecule: DNA (5'-D(P*CP*AP*AP*CP*AP*AP*CP*A)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 15 residues
Sequence: AACAACAACAACAAC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.752
R work: 0.1735
R free: 0.1996
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.1 M Phosphoric-citric acid pH 4.2 and 20% PEG300
Matthews coefficient: 2.2
Solvent content (%): 44.02
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: 2018-09-19
Crystal Structure of the Human CAMKK2B (PDB entry 5UYJ)
Macromolecule: Calcium/calmodulin-dependent protein kinase kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.17
Sequence length: 291 residues
Sequence: SMQLNQYTLKDEIGKGSYGVVKLAYNENDNTYYAMKVLSKKKLIRQAGFPRRPPPRGTRPAPGGCIQPRGPIEQVYQEIAILKKLDHPNVVKLVEVLDDPNEDHLYMVFELVNQGPVMEVPTLKPLSEDQARFYFQDLIKGIEYLHYQKIIHRDIKPSNLLVGEDGHIKIADFGVSNEFKGSDALLSNTVGTPAFMAPESLSETRKIFSGKALDVWAMGVTLYCFVFGQCPFMDERIMCLHSKIKSQALEFPDQPDIAEDLKDLITRMLDKNPESRIVVPEIKLHPWVTRH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.153
R free: 0.171
Average B factor: 22.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG 3350, 20 mM Ammonium Sulphate, 0.1M Citric acid-Hepes-CHES buffer system
Matthews coefficient: 2.43
Solvent content (%): 49.37
Ligand: 2-cyclopentyl-4-(7-methoxyquinolin-4-yl)benzoic acid (8R7)
Ligand formula: C22 H21 N O3
Ligand molecular weight: 347.407
Ligand SMILES: COc1ccc2c(ccnc2c1)c3ccc(c(c3)C4CCCC4)C(=O)O
Ligand InChI: InChI=1S/C22H21NO3/c1-26-16-7-9-18-17(10-11-23-21(18)13-16)15-6-8-19(22(24)25)20(12-15)14-4-2-3-5-14/h6-14H,2-5H2,1H3,(H,24,25)
Release date: 2017-04-26
BRAF Kinase domain b3aC loop deletion mutant in complex with sorafenib (PDB entry 5HI2)
Macromolecule: Serine/threonine-protein kinase B-raf
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 283 residues
Sequence: MHHHHHGSRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.512
R work: 0.1851
R free: 0.2371
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 292
Crystal growth procedure: 20% PEG 3350, and 0.2M Potassium Nitrate
Matthews coefficient: 2.24
Solvent content (%): 45.02
Ligand: 4-{4-[({[4-CHLORO-3-(TRIFLUOROMETHYL)PHENYL]AMINO}CARBONYL)AMINO]PHENOXY}-N-METHYLPYRIDINE-2-CARBOXAMIDE (BAX)
Ligand formula: C21 H16 Cl F3 N4 O3
Ligand molecular weight: 464.825
Ligand SMILES: CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl
Ligand InChI: InChI=1S/C21H16ClF3N4O3/c1-26-19(30)18-11-15(8-9-27-18)32-14-5-2-12(3-6-14)28-20(31)29-13-4-7-17(22)16(10-13)21(23,24)25/h2-11H,1H3,(H,26,30)(H2,28,29,31)
Release date: 2016-04-06
Discovery of TAK-659, an Orally Available Investigational Inhibitor of Spleen Tyrosine Kinase (SYK) (PDB entry 5TR6)
Macromolecule: Tyrosine-protein kinase SYK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 289 residues
Sequence: MALEEIRPKEVYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKNEANDPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVNHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.93
R work: 0.1933
R free: 0.2172
Average B factor: 35.14
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.1
Crystallization temperature (K): 293
Crystal growth procedure: 0.7M Potassium Na Tartrate, 0.06M MES_Na, 0.04M MES
Matthews coefficient: 2.43
Solvent content (%): 49.32
Ligand: 6-{[(1R,2S)-2-aminocyclohexyl]amino}-7-fluoro-4-(1-methyl-1H-pyrazol-4-yl)-1,2-dihydro-3H-pyrrolo[3,4-c]pyridin-3-one (7KG)
Ligand formula: C17 H21 F N6 O
Ligand molecular weight: 344.387
Ligand SMILES: Cn1cc(cn1)c2c3c(c(c(n2)NC4CCCCC4N)F)CNC3=O
Ligand InChI: InChI=1S/C17H21FN6O/c1-24-8-9(6-21-24)15-13-10(7-20-17(13)25)14(18)16(23-15)22-12-5-3-2-4-11(12)19/h6,8,11-12H,2-5,7,19H2,1H3,(H,20,25)(H,22,23)/t11-,12+/m0/s1
Release date: 2016-11-30
Crystal structure of human PCAF bromodomain in complex with compound SL1126 (compound 12) (PDB entry 5FE8)
Macromolecule: Histone acetyltransferase KAT2B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 119 residues
Sequence: SMGKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.19344
R free: 0.23252
Average B factor: 44.247
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277.15
Crystal growth procedure: 21-35% PEG 3350, 0.1 M Bis-Tris pH 5.5-7.0 or 21-40% medium-molecular-weight PEG smears (MMW PEG smears) buffered either with 0.1 M Bis-Tris pH 6.0-7.5 or 0.1 M Tris pH 7.5-8.8
Matthews coefficient: 3.36
Solvent content (%): 63.39
Ligand: ~{N}-(1,4-dimethyl-2-oxidanylidene-quinolin-7-yl)ethanamide (5WT)
Ligand formula: C13 H14 N2 O2
Ligand molecular weight: 230.262
Ligand SMILES: CC1=CC(=O)N(c2c1ccc(c2)NC(=O)C)C
Ligand InChI: InChI=1S/C13H14N2O2/c1-8-6-13(17)15(3)12-7-10(14-9(2)16)4-5-11(8)12/h4-7H,1-3H3,(H,14,16)
Release date: 2016-01-13
Crystal structure of HRas in complex with the Ras-binding and cysteine-rich domains of CRaf-kinase (PDB entry 7JHP)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 166 residues
Sequence: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYCEQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.766
R work: 0.211
R free: 0.2637
Average B factor: 50.88
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% w/v PEG10000
Matthews coefficient: 2.21
Solvent content (%): 44.42
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2020-08-05
CRYSTAL STRUCTURE OF PHD2 CATALYTIC DOMAIN (CID 7465) IN COMPLEX WITH AKB-6548 AT 1.8 A RESOLUTION (PDB entry 7UMP)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 216 residues
Sequence: LPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGMLVAQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.169
R free: 0.202
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 5.5
Crystallization temperature (K): 299
Crystal growth procedure: 100 MM SODIUM ACETATE PH 5.5, 21%
 PEG1500, 15% MPD, 300 MM MGSO4, 4 MM AKB-6548
Matthews coefficient: 2.97
Solvent content (%): 58.61
Ligand: FE (II) ION (FE2)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+2]
Ligand InChI: InChI=1S/Fe/q+2
Release date: 2022-05-18
Fragment-based inhibitors of Lipoprotein associated Phospholipase A2 (PDB entry 5LZ8)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: MAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.11
R work: 0.19415
R free: 0.25538
Average B factor: 36.07
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.4
Crystallization temperature (K): 293
Crystal growth procedure: 28.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7.4, 1.3M NaCl
Matthews coefficient: 2.28
Solvent content (%): 46.14
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: 2016-12-21
Crystal Structure of G Protein-Coupled Receptor Kinase 5 in Complex with Sangivamycin (PDB entry 4TNB)
Macromolecule: G protein-coupled receptor kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.16
Sequence length: 590 residues
Sequence: MELENIVANTVLLKAREGGGGKRKGKSKKWKEILKFPHISQCEDLRRTIDRDYCSLCDKQPIGRLLFRQFCETRPGLECYIQFLDSVAEYEVTPDEKLGEKGKKIMTKYLTPKSPVFIAQVGQDLVSQTEEKLLQKPCKELFSACAQSVHEYLRGEPFHEYLDSMFFDRFLQWKWLERQPVTKNTFRQYRVLGKGGFGEVCACQVRATGKMYACKRLEKKRIKKRKGESMALNEKQILEKVNSQFVVNLAYAYETKDALCLVLTIMNGGDLKFHIYNMGNPGFEEERALFYAAEILCGLEDLHHENTVYRDLKPENILLDDYGHIRISDLGLAVKIPEGDLIRGRVGTVGYMAPEVLNNQRYGLSPDYWGLGCLIYEMIEGQSPFRGRKEKVKREEVDRRVLETEEVYSHKFSEEAKSICKMLLTKDAKQRLGCQEEEAAEVKRHPFFRNMNFKRLEAGMLDPPFVPDPRAVYCKDVLDIEQFSTVKGVNLDHTDDDFYSKFSTGSVSIPWQNEMIETECFKELNVFGPNGTLPPDLNRNHPPEPPKKGLLQRLFKRQHQNNSKSSPSSKTSFNHHINSNHVSSNSTGSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.113
R work: 0.1703
R free: 0.2319
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 277
Crystal growth procedure: 21% PEG 3350, 0.15 M Sodium Chloride, 0.1 M BIS-TRIS pH 5.5
Matthews coefficient: 2.11
Solvent content (%): 41.74
Ligand: SANGIVAMYCIN (SGV)
Ligand formula: C12 H15 N5 O5
Ligand molecular weight: 309.278
Ligand SMILES: c1c(c2c(ncnc2n1C3C(C(C(O3)CO)O)O)N)C(=O)N
Ligand InChI: InChI=1S/C12H15N5O5/c13-9-6-4(10(14)21)1-17(11(6)16-3-15-9)12-8(20)7(19)5(2-18)22-12/h1,3,5,7-8,12,18-20H,2H2,(H2,14,21)(H2,13,15,16)/t5-,7-,8-,12-/m1/s1
Release date: 2015-06-10
Structure of the GEF Kalirin DH2 Domain (PDB entry 8C7D)
Macromolecule: Kalirin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 201 residues
Sequence: SMKNPEEEQKAKALRGRMFVLNELVQTEKDYVKDLGIVVEGFMKRIEEKGVPEDMRGKDKIVFGNIHQIYDWHKDFFLAELEKCIQEQDRLAQLFIKHERKLHIYVWYCQNKPRSEYIVAEYDAYFEEVKQEINQRLTLSDFLIKPIQRITKYQLLLKDFLRYSEKAGLECSDIEKAVELMCLVPKRCNDMMNLGRLQGFE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.86
R work: 0.2273
R free: 0.2745
Average B factor: 33.86
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20% W/V PEG3350, 0.1 M succinic acid
Matthews coefficient: 2.13
Solvent content (%): 42.13
Release date: 2024-01-24
Crystal structure of AKR1C3 in complex with DFV (PDB entry 8JP1)
Macromolecule: Aldo-keto reductase family 1 member C3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.1.1
Sequence length: 331 residues
Sequence: MDSKHQCVKLNDGHFMPVLGFGTYAPPEVPRSKALEVTKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWSTFHRPELVRPALENSLKKAQLDYVDLYLIHSPMSLKPGEELSPTDENGKVIFDIVDLCTTWEAMEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNRSKLLDFCKSKDIVLVAYSALGSQRDKRWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTAEDMKAIDGLDRNLHYFNSDSFASHPNYPYSDEYLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.2055
R free: 0.257
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 298
Crystal growth procedure: 15-20% (w/v) PEG 8000, 100 mM MES and 0.14 M NaCl
Matthews coefficient: 2.55
Solvent content (%): 51.79
Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP)
Ligand formula: C21 H28 N7 O17 P3
Ligand molecular weight: 743.405
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2024-04-24
Crystal structure of NTMT1 in complex with RPKRIA peptide (PDB entry 5E1O)
Macromolecule: N-terminal Xaa-Pro-Lys N-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.244
Sequence length: 241 residues
Sequence: MGSSHHHHHHSSGLVPRGSTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.1512
R free: 0.1888
Average B factor: 21.142
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 26% PEG3350, 16% tacsimate
Matthews coefficient: 3.06
Solvent content (%): 59.86
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: 2015-10-28