satarupa22/MacromolecularLigandDB huggingface dataset:
Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP244 (PDB entry 6BMU)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 526 residues
Sequence: SMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.12
R work: 0.181
R free: 0.225
Average B factor: 42.56
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 17% PEG3350, 200MM AMMONIUM PHOSPHATE
Matthews coefficient: 2.27
Solvent content (%): 45.73
Ligand: 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine (5OD)
Ligand formula: C16 H19 Cl2 N5
Ligand molecular weight: 352.262
Ligand SMILES: CC1(CCN(CC1)c2cnc(c(n2)N)c3cccc(c3Cl)Cl)N
Ligand InChI: InChI=1S/C16H19Cl2N5/c1-16(20)5-7-23(8-6-16)12-9-21-14(15(19)22-12)10-3-2-4-11(17)13(10)18/h2-4,9H,5-8,20H2,1H3,(H2,19,22)
Release date: 2018-01-17
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1216861874 (PDB entry 7G8J)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.986
R work: 0.2268
R free: 0.2813
Average B factor: 36.78
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.49
Solvent content (%): 50.67
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: 2023-07-12
Human carbonic anhydrase II in complex with 2,3,5,6-tetrafluoro-4-(2-hydroxyethylsulfanyl)-N-methyl-benzenesulfonamide (PDB entry 7AEQ)
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): 1.5
R work: 0.1723
R free: 0.2137
Average B factor: 22.285
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)
Matthews coefficient: 2.05
Solvent content (%): 40.01
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: 2021-09-01
LSD1-CoREST-S2116 N5 adduct model (PDB entry 6KGN)
Macromolecule: Lysine-specific histone demethylase 1A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1
Sequence length: 669 residues
Sequence: GPLGSHMSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAM
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.62
R work: 0.1751
R free: 0.1944
Average B factor: 90.35
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate
Matthews coefficient: 7.02
Solvent content (%): 82.47
Ligand: FLAVIN-ADENINE DINUCLEOTIDE (FAD)
Ligand formula: C27 H33 N9 O15 P2
Ligand molecular weight: 785.55
Ligand SMILES: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
Ligand InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
Release date: 2020-03-25
JAK2 JH1 in complex with PN4-073 (PDB entry 6VNK)
Macromolecule: Tyrosine-protein kinase JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 308 residues
Sequence: HHHHHHHHENLYFQGDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.2183
R free: 0.2442
Average B factor: 51.6178
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1 M Bis-Tris pH 5.5, 0.2 M NaCl, 25% PEG 3350
Matthews coefficient: 3.04
Solvent content (%): 59.56
Ligand: (3R)-3-cyclopentyl-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile (RXT)
Ligand formula: C17 H18 N6
Ligand molecular weight: 306.365
Ligand SMILES: c1c[nH]c2c1c(ncn2)c3cnn(c3)C(CC#N)C4CCCC4
Ligand InChI: InChI=1S/C17H18N6/c18-7-5-15(12-3-1-2-4-12)23-10-13(9-22-23)16-14-6-8-19-17(14)21-11-20-16/h6,8-12,15H,1-5H2,(H,19,20,21)/t15-/m1/s1
Release date: 2021-02-17
X-ray structure of furin in complex with the inhibitory antibody Nb14 (PDB entry 5JMO)
Macromolecule: CMK-inhibitor
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 6 residues
Sequence: XRVKRX
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.998
R work: 0.163
R free: 0.1971
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: .1 M sodium acetate, pH 5.6, 16-18% PEG 3350
Matthews coefficient: 2.33
Solvent content (%): 47.2
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2016-12-07
Tricomplex of RMC-7977, KRAS G12C, and CypA (PDB entry 8TBK)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 166 residues
Sequence: SMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.26
R work: 0.1462
R free: 0.1839
Average B factor: 25.86
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 27% PEG4000, 0.1 M imidazole, pH 7.0
Matthews coefficient: 2.31
Solvent content (%): 46.74
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2024-02-07
HUMAN JAK1 IN COMPLEX WITH LASW1393 (PDB entry 6HZU)
Macromolecule: Tyrosine-protein kinase JAK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 302 residues
Sequence: GDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.20058
R free: 0.26545
Average B factor: 28.682
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 30 % PEG6000_50
0.10 M MES pH 6.00
Matthews coefficient: 2.45
Solvent content (%): 49.79
Ligand: 2-[4-[8-oxidanylidene-2-[(~{E})-(2-oxidanylidenepyridin-3-ylidene)amino]-7~{H}-purin-9-yl]cyclohexyl]ethanenitrile (GYQ)
Ligand formula: C18 H17 N7 O2
Ligand molecular weight: 363.373
Ligand SMILES: c1c2c(nc(n1)N=C3C=CC=NC3=O)N(C(=O)N2)C4CCC(CC4)CC#N
Ligand InChI: InChI=1S/C18H17N7O2/c19-8-7-11-3-5-12(6-4-11)25-15-14(23-18(25)27)10-21-17(24-15)22-13-2-1-9-20-16(13)26/h1-2,9-12H,3-7H2,(H,23,27)/b22-13+/t11-,12-
Release date: 2019-10-23
Structure of Ku80 von Willebrand domain complexed with MRI Ku Binding Motif (PDB entry 6TYU)
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: MHHHHHHMARAAKSAVVLCMDVGLAMSHSNQGKESPFEQAKKVMMLFLQRQVFAESKDEIAVVLYGTDTTDNALAREDQYENISVHRHLMLPDFDLLEQIENVVEPGSVQADFLDALIVSMDLLQKETLGKKYTRLHIAVFSDLSSPFSVDQLEVIIANLKKAEITLQFFLPFSVDEGSGPGKGLSDQQKEGIEMVRKIMFSLDGEEGLSEVFTFRDSLERLSIFKKIERR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46862727205
R work: 0.178048002916
R free: 0.200770793241
Average B factor: 32.8655062593
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 0.2 M Potassium formate, 20 % (w/v) PEG3350
Matthews coefficient: 2.11
Solvent content (%): 41.71
Release date: 2019-11-27
Factor Xa complex with GTC000101 (PDB entry 4Y6D)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.6
Sequence length: 254 residues
Sequence: IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKAKSHAPEVITSSPLK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1985
R free: 0.2334
Average B factor: 28.035
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 16-20% PEG 6K, 50mM Mes-NaOH pH 5.7-6.0, 5 mM CaCl2, and 50 mM NaCl
Matthews coefficient: 1.86
Solvent content (%): 33.75
Ligand: 4-[(3S)-3-({[(E)-2-(5-chlorothiophen-2-yl)ethenyl]sulfonyl}amino)-2-oxopyrrolidin-1-yl]-3-fluoro-N,N-dimethylbenzamide (48U)
Ligand formula: C19 H19 Cl F N3 O4 S2
Ligand molecular weight: 471.953
Ligand SMILES: CN(C)C(=O)c1ccc(c(c1)F)N2CCC(C2=O)NS(=O)(=O)C=Cc3ccc(s3)Cl
Ligand InChI: InChI=1S/C19H19ClFN3O4S2/c1-23(2)18(25)12-3-5-16(14(21)11-12)24-9-7-15(19(24)26)22-30(27,28)10-8-13-4-6-17(20)29-13/h3-6,8,10-11,15,22H,7,9H2,1-2H3/b10-8+/t15-/m0/s1
Release date: 2015-09-30
The Crystal Structure of Human Neuropeptide Y Y2 Receptor with JNJ-31020028 (PDB entry 7DDZ)
Macromolecule: Human Neuropeptide Y Y2 Receptor fusion protein
Type: Protein, polypeptide(L)
Source organism: Enterobacteria phage RB59
EC number: 3.2.1.17
Sequence length: 665 residues
Sequence: GAPNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYMGPIGAEADENQTVEEMKVEQYGPQTTPRGELVPDPEPELIDSTKLIEVQVVLILAYCSIILLGVIGNSLVIHVVIKFKSMRTVTNFFIANLAVADLLVNTLCLPFTLTYTLMGEWKMGPVLCHLVPYAQGLAVQVSTITLTVIALDRYRCIVYHLESKISKRISFLIIGLAWGISALLASPLAIFREYSLIEIIPDFEIVACTEKWPGEEKSIYGTVYSLSSLLILYVLPLGIISFSYTRIWSKLKNHVAKALIVYGSTTGNTEYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSIELQDDFIPLFDSLEETGAQGRKVACFGCGDSSWEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARDDIVGWAHDVRGAIDHYHQRRQKTTKMLVCVVVVFAVCWLPLHAFQLAVDIDSQVLDLKEYKLIFTVFHIIAMCSTFANPLLYGWMNSNYRKAFLSAFRCEQRLDAIHSEVEFLEVLFQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2548
R free: 0.2891
Average B factor: 71.06
Crystallization method: LIPIDIC CUBIC PHASE
Crystallization temperature (K): 293.15
Crystal growth procedure: 0.1 M HEPES, pH 7.0-7.5, 250-350 mM (NH4)2SO4, and 20-30% PEG500DME, or 0.1 M MES, pH 6.0-6.5, 380-420 mM NH4 tartrate, and 24-26% PEG500DME
Matthews coefficient: 4.66
Solvent content (%): 73.58
Ligand: ~{N}-[4-[4-[(1~{S})-2-(diethylamino)-2-oxidanylidene-1-phenyl-ethyl]piperazin-1-yl]-3-fluoranyl-phenyl]-2-pyridin-3-yl-benzamide (H46)
Ligand formula: C34 H36 F N5 O2
Ligand molecular weight: 565.68
Ligand SMILES: CCN(CC)C(=O)C(c1ccccc1)N2CCN(CC2)c3ccc(cc3F)NC(=O)c4ccccc4c5cccnc5
Ligand InChI: InChI=1S/C34H36FN5O2/c1-3-38(4-2)34(42)32(25-11-6-5-7-12-25)40-21-19-39(20-22-40)31-17-16-27(23-30(31)35)37-33(41)29-15-9-8-14-28(29)26-13-10-18-36-24-26/h5-18,23-24,32H,3-4,19-22H2,1-2H3,(H,37,41)/t32-/m0/s1
Release date: 2021-01-27
MTH1 in complex with compound 32 (PDB entry 6US4)
Macromolecule: 7,8-dihydro-8-oxoguanine triphosphatase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.55
Sequence length: 159 residues
Sequence: GSHMGASRLYTLVLVLQPQRVLLGMKKRGFGAGRWNGFGGKVQEGETIEDGARRELQEESGLTVDALHKVGQIVFEFVGEPELMDVHVFCTDSIQGTPVESDEMRPCWFQLDQIPFKDMWPDDSYWFPLLLQKKKFHGYFKFQGQDTILDYTLREVDTV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95032907402
R work: 0.175057190813
R free: 0.244401912066
Average B factor: 21.2333500652
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 30% PEG 6000, 0.1M sodium acetate pH 4.0, 0.2M lithium sulfate
Matthews coefficient: 1.99
Solvent content (%): 38.06
Ligand: 5-(2,3-dichlorophenyl)[1,2,4]triazolo[1,5-a]pyridin-2-amine (GN6)
Ligand formula: C12 H8 Cl2 N4
Ligand molecular weight: 279.125
Ligand SMILES: c1cc(c(c(c1)Cl)Cl)c2cccc3n2nc(n3)N
Ligand InChI: InChI=1S/C12H8Cl2N4/c13-8-4-1-3-7(11(8)14)9-5-2-6-10-16-12(15)17-18(9)10/h1-6H,(H2,15,17)
Release date: 2020-04-01
Ask1 bound to compound 28 (PDB entry 7MU6)
Macromolecule: Mitogen-activated protein kinase kinase kinase 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.25
Sequence length: 334 residues
Sequence: MDYKDDDDKENLYFQGSTEEGDCESDLLEYDYEYDENGDRVVLGKGTYGIVYAGRDLSNQVRIAIKEIPERDSRYSQPLHEEIALHKHLKHKNIVQYLGSFSENGFIKIFMEQVPGGSLSALLRSKWGPLKDNEQTIGFYTKQILEGLKYLHDNQIVHRDIKGDNVLINTYSGVLKISDFGTSKRLAGINPCTEEFTGTLQYMAPEIIDKGPRGYGKAADIWSLGCTIIEMATGKPPFYELGEPQAAMFKVGMFKVHPEIPESMSAEAKAFILKCFEPDPDKRACANDLLVDEFLKVSSKKKKTQPKLSALSAGSNEYLRSISLPVPVLVEDTS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.165
R work: 0.1895
R free: 0.2144
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.1M BisTRIS pH 5.5, 0.2M ammonium acetate, 3% sorbitol and 12% PEG3350
Matthews coefficient: 2.49
Solvent content (%): 50.51
Ligand: 2-methoxy-N-(6-{4-[(2S)-1,1,1-trifluoropropan-2-yl]-4H-1,2,4-triazol-3-yl}pyridin-2-yl)pyridine-3-carboxamide (A1AWT)
Ligand formula: C17 H15 F3 N6 O2
Ligand molecular weight: 392.335
Ligand SMILES: CC(C(F)(F)F)n1cnnc1c2cccc(n2)NC(=O)c3cccnc3OC
Ligand InChI: InChI=1S/C17H15F3N6O2/c1-10(17(18,19)20)26-9-22-25-14(26)12-6-3-7-13(23-12)24-15(27)11-5-4-8-21-16(11)28-2/h3-10H,1-2H3,(H,23,24,27)/t10-/m0/s1
Release date: 2024-07-17
Crystal structure of the dihydroorotase domain (K1556A) of human CAD (PDB entry 5YNZ)
Macromolecule: CAD protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.5.5
Sequence length: 391 residues
Sequence: MTSQKLVRLPGLIDVHVHLREPGGTHKEDFASGTAAALAGGITMVCAMPNTRPPIIDAPALALAQKLAEAGARCDFALFLGASSENAGTLGTVAGSAAGLALYLNETFSELRLDSVVQWMEHFETWPSHLPIVAHAEQQTVAAVLMVAQLTQRSVHICHVARKEEILLIKAAKARGLPVTCEVAPHHLFLSHDDLERLGPGKGEVRPELGSRQDVEALWENMAVIDCFASDHAPHTLEEKCGSRPPPGFPGLETMLPLLLTAVSEGRLSLDDLLQRLHHNPRRIFHLPPQEDTYVEVDLEHEWTIPSHMPFSKAHWTPFEGQKVKGTVRRVVLRGEVAYIDGQVLVPPGYGQDVRKWPQGAVPQLPPSAPATSEMTTTPERPRRGIPGLPD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.774
R work: 0.226
R free: 0.2889
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 2M sodium chloride, 100mM MES sodium salt pH6.5, 200mM sodium acetate
Matthews coefficient: 2.81
Solvent content (%): 56.16
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: 2018-10-24
Crystal structure of human DNA polymerase eta incorporating ITP across dT (PDB entry 8G8J)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 432 residues
Sequence: MATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.74
R work: 0.2114
R free: 0.2452
Average B factor: 36.66
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM MES, pH 6.5, 20% PEG2000 MME, 5 mM calcium chloride
Matthews coefficient: 2.12
Solvent content (%): 41.97
Ligand: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (CZU)
Ligand formula: C10 H15 N4 O14 P3
Ligand molecular weight: 508.166
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=CNC2=O
Ligand InChI: InChI=1S/C10H15N4O14P3/c15-6-4(1-25-30(21,22)28-31(23,24)27-29(18,19)20)26-10(7(6)16)14-3-13-5-8(14)11-2-12-9(5)17/h2-4,6-7,10,15-16H,1H2,(H,21,22)(H,23,24)(H,11,12,17)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
Release date: 2024-02-21
Tri-complex of Compound-3, KRAS G12V, and CypA (PDB entry 9BG1)
Macromolecule: GTPase KRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 170 residues
Sequence: SMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.51
R work: 0.1874
R free: 0.2264
Average B factor: 20.34
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
Matthews coefficient: 2.24
Solvent content (%): 44.97
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2024-06-12
Crystal structure of PTP1B D181A/Q262A phosphatase domain with TYK2 activation loop phosphopeptide (PDB entry 8EXN)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 299 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPCRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTCGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPAFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIATADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDL
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.151
R work: 0.2177
R free: 0.2408
Average B factor: 64.5384
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281.15
Crystal growth procedure: 0.2 M Calcium Acetate, 12.5% PEG 4K, 0.05 M MES (pH 6.5)
Matthews coefficient: 3.64
Solvent content (%): 66.17
Ligand: PHOSPHATE ION (PO4)
Ligand formula: O4 P
Ligand molecular weight: 94.971
Ligand SMILES: [O-]P(=O)([O-])[O-]
Ligand InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
Release date: 2023-07-05
Structural basis of the recognition of H3K36me3 by DNMT3B PWWP domain (PDB entry 5CIU)
Macromolecule: DNA (cytosine-5)-methyltransferase 3B
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.37
Sequence length: 150 residues
Sequence: EADSGDGDSSEYQDGKEFGIGDLVWGKIKGFSWWPAMVVSWKATSKRQAMSGMRWVQWFGDGKFSEVSADKLVALGLFSQHFNLATFNKLVSYRKAMYHALEKARVRAGKTFPSSPGDSLEDQLKPMLEWAHGGFKPTGIEGLKPNNTQP
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.24
R work: 0.2241
R free: 0.2588
Average B factor: 46.45
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M SODIUM CITRATE TRIBASIC
Matthews coefficient: 3.35
Solvent content (%): 63.3
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: 2016-03-30