satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of human phosphodiesterase 10 in complex with 3,6-dimethyl-N-(2-phenylimidazo[1,2-a]pyrimidin-7-yl)pyridine-2-carboxamide (PDB entry 5SIR)
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): 2.5
R work: 0.1859
R free: 0.2216
Average B factor: 46.147
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: 2.67
Solvent content (%): 53.9
Ligand: 3,6-dimethyl-N-[(4R)-2-phenylimidazo[1,2-a]pyrimidin-7-yl]pyridine-2-carboxamide (JSF)
Ligand formula: C20 H17 N5 O
Ligand molecular weight: 343.382
Ligand SMILES: Cc1ccc(nc1C(=O)Nc2ccn3cc(nc3n2)c4ccccc4)C
Ligand InChI: InChI=1S/C20H17N5O/c1-13-8-9-14(2)21-18(13)19(26)23-17-10-11-25-12-16(22-20(25)24-17)15-6-4-3-5-7-15/h3-12H,1-2H3,(H,22,23,24,26)
Release date: 2022-10-12
Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: ground state at pH7.0 (K+ MES) with 1 Ca2+ ion (PDB entry 5KFM)
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): 1.6
R work: 0.1941
R free: 0.234
Average B factor: 28.7414
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 (%): 41.15
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2016-06-22
Structure of human GGT1 in complex with Lnt2-65 compound (PDB entry 7LBC)
Macromolecule: Glutathione hydrolase 1 heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.13
Sequence length: 353 residues
Sequence: SASKEPDNHVYTRAAVAADAKQCSKIGRDALRDGGSAVDAAIAALLCVGLMNAHSMGIGGGLFLTIYNSTTRKAEVINAREVAPRLAFATMFNSSEQSQKGGLSVAVPGEIRGYELAHQRHGRLPWARLFQPSIQLARQGFPVGKGLAAALENKRTVIEQQPVLCEVFCRDRKVLREGERLTLPQLADTYETLAIEGAQAFYNGSLTAQIVKDIQAAGGIVTAEDLNNYRAELIEHPLNISLGDAVLYMPSAPLSGPVLALILNILKGYNFSRESVESPEQKGLTYHRIVEAFRFAYAKRTLLGDPKFVDVTEVVRNMTSEFFAAQLRAQISDDTTHPISYYKPEFYTPDDGG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.2494
R free: 0.3057
Average B factor: 47.437
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 295
Crystal growth procedure: 22% PEG 3350, 0.1M ammonium chloride, 0.1M sodium cacodylate
Matthews coefficient: 2.89
Solvent content (%): 57.44
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: 2022-02-09
Aerobic crystal structure of HIF prolyl hydroxylase 2 (PHD2 181-407) in complex with Fe(III), 2-oxoglutarate (2OG) and HIF2alpha-CODD peptide (PDB entry 8Q6E)
Macromolecule: Egl nine homolog 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.11.29
Sequence length: 233 residues
Sequence: GSHMASPNGQTKPLPALKLALEYIVPCMNKHGICVVDDFLGKETGQQIGDEVRALHDTGKFTDGQLVSQKSDSSKDIRGDKITWIEGKEPGCETIGLLMSSMDDLIRHCNGKLGSYKINGRTKAMVACYPGNGTGYVRHVDNPNGDGRCVTCIYYLNKDWDAKVSGGILRIFPEGKAQFADIEPKFDRLLFFWSDRRNPHEVQPAYATRYAITVWYFDADERARAKVKYLTGE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.37
R work: 0.1797
R free: 0.2053
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: (10-35%) PEG 4K, 0.2 M ammonium acetate , 0.1 M sodium ammonium acetate trihydrate pH (4.1-5.6)
Matthews coefficient: 1.88
Solvent content (%): 34.65
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: 2024-08-21
Structure of CDK12/CycK in complex with a small molecule inhibitor N-(4-(1-methyl-1H-pyrazol-4-yl)phenyl)-N-((1r,4r)-4-(quinazolin-2-ylamino)cyclohexyl)acetamide (PDB entry 6CKX)
Macromolecule: Cyclin-dependent kinase 12
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 351 residues
Sequence: GQTESDWGKRCVDKFDIIGIIGEGTYGQVYKAKDKDTGELVALKKVRLDNEKEGFPITAIREIKILRQLIHRSVVNMKEIVTDKQDALDFKKDKGAFYLVFEYMDHDLMGLLESGLVHFSEDHIKSFMKQLMEGLEYCHKKNFLHRDIKCSNILLNNSGQIKLADFGLARLYNSEESRPYTNKVITLWYRPPELLLGEERYTPAIDVWSCGCILGELFTKKPIFQANLELAQLELISRLCGSPCPAVWPDVIKLPYFNTMKPKKQYRRRLREEFSFIPSAALDLLDHMLTLDPSKRCTAEQTLQSDFLKDVELSKMAPPDLPHWQDCHELWSKKRRRQRQSGVVVEEPPPS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.208
R free: 0.251
Average B factor: 85.84
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1 M HEPES (PH 6.5), 18% PEG 3350,
 0.2 M MGCL2, AND 1 MM SARCOSINE, VAPOR DIFFUSION, HANGING DROP,
 TEMPERATURE 297K
Matthews coefficient: 2.49
Solvent content (%): 50.56
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: 2018-08-29
Crystal structure of c-MET bound by compound 5 (PDB entry 7B3Z)
Macromolecule: Hepatocyte growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 299 residues
Sequence: GNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.193
R free: 0.215
Average B factor: 37.64
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 20 % PEG10000, 0.1 M Na-HEPES pH 7.5
Matthews coefficient: 2.54
Solvent content (%): 51.5
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: 2020-12-09
TrkA JM-kinase with {N}-(2-pyridylmethyl)-2-[2-(2-thienyl)indol-1-yl]acetamide (PDB entry 5KMJ)
Macromolecule: High affinity nerve growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 329 residues
Sequence: SSLSPTEGKGSGLQGHIIENPQYFSDACVHHIKRRDIVLKWELGEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGDLNRFLRSHGPDAKLLAGGEDVAPGPLGLGQLLAVASQVAAGMVYLAGLHFVHRDLATRNCLVGQGLVVKIGDFGMSRDIYSTDYYRVGGRTMLPIRWMPPESILYRKFTTESDVWSFGVVLWEIFTYGKQPWYQLSNTEAIDCITQGRELERPRACPPEVYAIMRGCWQREPQQRHSIKDVHARLQALAQAPPVYLDVLGHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.04
R work: 0.194
R free: 0.2257
Average B factor: 39.05
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 50mM MES pH 6.5, 150 mM NaCl, 5mM TCEP, 0.1% beta-OctylGlucoside
Matthews coefficient: 2.39
Solvent content (%): 48.46
Ligand: ~{N}-(pyridin-2-ylmethyl)-2-(2-thiophen-2-ylindol-1-yl)ethanamide (6UF)
Ligand formula: C20 H17 N3 O S
Ligand molecular weight: 347.433
Ligand SMILES: c1ccc2c(c1)cc(n2CC(=O)NCc3ccccn3)c4cccs4
Ligand InChI: InChI=1S/C20H17N3OS/c24-20(22-13-16-7-3-4-10-21-16)14-23-17-8-2-1-6-15(17)12-18(23)19-9-5-11-25-19/h1-12H,13-14H2,(H,22,24)
Release date: 2016-12-28
XChem group deposition -- Crystal Structure of human ACVR1 in complex with FM010913a (PDB entry 5S75)
Macromolecule: Activin receptor type-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.30
Sequence length: 301 residues
Sequence: SMQRTVARDITLLECVGKGRYGEVWRGSWQGENVAVKIFSSRDEKSWFRETELYNTVMLRHENILGFIASDMTSRHSSTQLWLITHYHEMGSLYDYLQLTTLDTVSCLRIVLSIASGLAHLHIEIFGTQGKPAIAHRDLKSKNILVKKNGQCCIADLGLAVMHSQSTNQLDVGNNPRVGTKRYMAPEVLDETIQVDCFDSYKRVDIWAFGLVLWEVARRMVSNGIVEDYKPPFYDVVPNDPSFEDMRKVVCVDQQRPNIPNRWFSDPTLTSLAKLMKECWYQNPSARLTALRIKKTLTKID
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.155
R free: 0.1729
Average B factor: 17.822
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6
Crystallization temperature (K): 277
Crystal growth procedure: 0.1M citrate pH 6.0, 1.4M ammonium sulfate, 0.2M sodium/potassium tartrate
Matthews coefficient: 2.6
Solvent content (%): 52.65
Ligand: 4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine (LU8)
Ligand formula: C27 H32 N2 O3
Ligand molecular weight: 432.555
Ligand SMILES: Cc1c(cncc1c2cc(c(c(c2)OC)OC)OC)c3ccc(cc3)C4CCN(CC4)C
Ligand InChI: InChI=1S/C27H32N2O3/c1-18-23(21-8-6-19(7-9-21)20-10-12-29(2)13-11-20)16-28-17-24(18)22-14-25(30-3)27(32-5)26(15-22)31-4/h6-9,14-17,20H,10-13H2,1-5H3
Release date: 2021-06-23
Crystal structure of insulin degrading enzyme complexed with inhibitor tert-butyl [(2S)-2-(2,5-difluorophenyl)-3-(quinolin-3-yl)propyl]carbamate (PDB entry 4PES)
Macromolecule: Ala-Ala-Ala
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 3 residues
Sequence: AAA
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.21
R work: 0.20884
R free: 0.25606
Average B factor: 46.756
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 298
Crystal growth procedure: 20% PEG3350, 0.2 mM sodium thiocyanate
Matthews coefficient: 2.44
Solvent content (%): 49.68
Ligand: tert-butyl [(2S)-2-(2,5-difluorophenyl)-3-(quinolin-3-yl)propyl]carbamate (2PJ)
Ligand formula: C23 H24 F2 N2 O2
Ligand molecular weight: 398.446
Ligand SMILES: CC(C)(C)OC(=O)NCC(Cc1cc2ccccc2nc1)c3cc(ccc3F)F
Ligand InChI: InChI=1S/C23H24F2N2O2/c1-23(2,3)29-22(28)27-14-17(19-12-18(24)8-9-20(19)25)11-15-10-16-6-4-5-7-21(16)26-13-15/h4-10,12-13,17H,11,14H2,1-3H3,(H,27,28)/t17-/m1/s1
Release date: 2015-06-17
Protein kinase MKK7 in complex with phenethyltriazole-substituted pyrazolopyrimidine (PDB entry 7OVI)
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: 318 residues
Sequence: MGHHHHHHSAKQTGYLTIGGQRYQAEINDLENLGEMGSGTCGQVWKMRFRKTGHVIAVKQMRRSGNKEENKRILMDLDVVLKSHDCPYIVQCFGTFITNTDVFIAMELMGTCAEKLKKRMQGPIPERILGKMTVAIVKALYYLKEKHGVIHRDVKPSNILLDERGQIKLCDFGISGRLVDSKAKTRSAGCAAYMAPERIDPPDPTKPDYDIRADVWSLGISLVELATGQFPYKNCKTDFEVLTKVLQEEPPLLPGHMGFSGDFQSFVKDCLTKDHRKRPKYNKLLEHSFIKRYETLEVDVASWFKDVMAKTESPRTSG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.2092
R free: 0.2504
Average B factor: 58.2
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 180-220 mM sodium citrate,
15-25 % PEG3350
Matthews coefficient: 2.46
Solvent content (%): 49.91
Ligand: 1-[(3~{R})-3-[4-azanyl-3-[1-(2-phenylethyl)-1,2,3-triazol-4-yl]pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one (2GI)
Ligand formula: C23 H27 N9 O
Ligand molecular weight: 445.52
Ligand SMILES: CCC(=O)N1CCCC(C1)n2c3c(c(n2)c4cn(nn4)CCc5ccccc5)c(ncn3)N
Ligand InChI: InChI=1S/C23H27N9O/c1-2-19(33)30-11-6-9-17(13-30)32-23-20(22(24)25-15-26-23)21(28-32)18-14-31(29-27-18)12-10-16-7-4-3-5-8-16/h3-5,7-8,14-15,17H,2,6,9-13H2,1H3,(H2,24,25,26)/t17-/m1/s1
Release date: 2022-07-20
Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine (PDB entry 4YPD)
Macromolecule: Death-associated protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 294 residues
Sequence: TVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDIEREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLKQILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTPEFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYFSNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSSAWSHPQFEK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.4
R work: 0.1551
R free: 0.1772
Average B factor: 24.216
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M HEPES, 1.7 M ammonium sulfate
Matthews coefficient: 1.91
Solvent content (%): 35.63
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: 2015-05-13
Human angiogenin ALS variant F100I (PDB entry 5M9R)
Macromolecule: Angiogenin
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.27
Sequence length: 124 residues
Sequence: MQDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICENKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGIRNVVVACENGLPVHLDQSIFRRP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.44
R work: 0.17232
R free: 0.19544
Average B factor: 12.679
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 289
Crystal growth procedure: 0.2 M Na/K tartrate
0.1 M Na cacodylate
20% PEG 4000
Matthews coefficient: 1.97
Solvent content (%): 37.62
Ligand: D(-)-TARTARIC ACID (TAR)
Ligand formula: C4 H6 O6
Ligand molecular weight: 150.087
Ligand SMILES: C(C(C(=O)O)O)(C(=O)O)O
Ligand InChI: InChI=1S/C4H6O6/c5-1(3(7)8)2(6)4(9)10/h1-2,5-6H,(H,7,8)(H,9,10)/t1-,2-/m0/s1
Release date: 2017-02-22
Human Sirt6 in complex with the inhibitor S6039 and ADP-ribose (PDB entry 8BL1)
Macromolecule: NAD-dependent protein deacetylase sirtuin-6
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.286
Sequence length: 302 residues
Sequence: GIDPFTADKGKCGLPEIFDPPEELERKVWELARLVWQSSSVVFHTGAGISTASGIPDFRGPHGVWTMEERGLAPKFDTTFESARPTQTHMALVQLERVGLLRFLVSQNVDGLHVRSGFPRDKLAELHGNMFVEECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGELRDTILDWEDSLPDRDLALADEASRNADLSITLGTSLQIRPSGNLPLATKRRGGRLVIVNLQPTKHDRHADLRIHGYVDEVMTRLMKHLGLEIPAWDGPRVLERALPPLPRPPTPKLEPKEESPTRIN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.06
R work: 0.1783
R free: 0.2163
Average B factor: 41.867
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.7
Crystallization temperature (K): 293
Crystal growth procedure: 1.6 M (NH4)2SO4, 10% PEG 400, and Bis-Tris buffer pH 5.7
Matthews coefficient: 2.65
Solvent content (%): 53.68
Ligand: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL
[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE (AR6)
Ligand formula: C15 H23 N5 O14 P2
Ligand molecular weight: 559.316
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Ligand InChI: InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
Release date: 2023-11-22
Crystal Structure of HRasQ61L(GMPPNP-bound) in complex with the Ras-binding domain(RBD) of SIN1 (PDB entry 7VV8)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 167 residues
Sequence: SMTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGLEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1796
R free: 0.1988
Average B factor: 27.1099
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: PEG20000, 0.1M Sodim citrate. pH 5.0
Matthews coefficient: 3.2
Solvent content (%): 61.58
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: 2022-05-18
Protease Inhibitor (PDB entry 5UGG)
Macromolecule: Plasminogen
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.7
Sequence length: 251 residues
Sequence: EFAPSFDCGKPQVEPKKCPGRVVGGCVAHPHSWPWQVSLRTRFGMHFCGGTLISPEWVLTAAHCLEKSPRPSSYKVILGAHQEVNLEPHVQEIEVSRLFLEPTRKDIALLKLSSPAVITDKVIPACLPSPNYVVADRTECFITGWGETQGTFGAGLLKEAQLPVIENKVCNRYEFLNGRVQSTELCAGHLAGGTDSCQGDSGGPLVCFEKDKYILQGVTSWGLGCARPNKPGVYVRVSRFVTWIEGVMRNN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.2
R work: 0.164
R free: 0.176
Average B factor: 14.55
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5
Crystallization temperature (K): 293
Crystal growth procedure: 10 % (w/v) polyethylene glycol 6,000, 
4 % (v/v) 2-methyl-2,4-pentanediol,
0.1M (2-(N-morpholino)ethanesulfonic acid)
Matthews coefficient: 2.05
Solvent content (%): 39.93
Ligand: Nalpha-[trans-4-(aminomethyl)cyclohexane-1-carbonyl]-N-octyl-O-[(quinolin-2-yl)methyl]-L-tyrosinamide (89M)
Ligand formula: C35 H48 N4 O3
Ligand molecular weight: 572.781
Ligand SMILES: CCCCCCCCNC(=O)C(Cc1ccc(cc1)OCc2ccc3ccccc3n2)NC(=O)C4CCC(CC4)CN
Ligand InChI: InChI=1S/C35H48N4O3/c1-2-3-4-5-6-9-22-37-35(41)33(39-34(40)29-16-12-27(24-36)13-17-29)23-26-14-20-31(21-15-26)42-25-30-19-18-28-10-7-8-11-32(28)38-30/h7-8,10-11,14-15,18-21,27,29,33H,2-6,9,12-13,16-17,22-25,36H2,1H3,(H,37,41)(H,39,40)/t27-,29-,33-/m0/s1
Release date: 2017-05-31
Wild type EGFR in complex with LN2380 (PDB entry 6VH4)
Macromolecule: Epidermal growth factor receptor
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: GEAPNQALLRILKETEFKKIKVLGSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCLLDYVREHKDNIGSQYLLNWCVQIAKGMNYLEDRRLVHRDLAARNVLVKTPQHVKITDFGLAKLLGAEEKEYHAEGGKVPIKWMALESILHRIYTHQSDVWSYGVTVWELMTFGSKPYDGIPASEISSILEKGERLPQPPICTIDVYMIMVKCWMIDADSRPKFRELIIEFSKMARDPQRYLVIQGDERMHLPSPTDSNFYRALMDEEDMDDVVDADEYLIPQQG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.1952
R free: 0.23
Average B factor: 58.1335
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 298
Crystal growth procedure: 1.4 M Sodium Citrate, 0.1 M MES
Matthews coefficient: 3.51
Solvent content (%): 65
Ligand: N-[3-({4-[4-(4-fluorophenyl)-2-(3-hydroxypropyl)-1H-imidazol-5-yl]pyridin-2-yl}amino)-4-methoxyphenyl]propanamide (QQM)
Ligand formula: C27 H28 F N5 O3
Ligand molecular weight: 489.541
Ligand SMILES: CCC(=O)Nc1ccc(c(c1)Nc2cc(ccn2)c3c(nc([nH]3)CCCO)c4ccc(cc4)F)OC
Ligand InChI: InChI=1S/C27H28FN5O3/c1-3-25(35)30-20-10-11-22(36-2)21(16-20)31-24-15-18(12-13-29-24)27-26(17-6-8-19(28)9-7-17)32-23(33-27)5-4-14-34/h6-13,15-16,34H,3-5,14H2,1-2H3,(H,29,31)(H,30,35)(H,32,33)
Release date: 2020-04-22
PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with FMOPL000706a (PDB entry 5QGJ)
Macromolecule: Peroxisomal coenzyme A diphosphatase NUDT7
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1
Sequence length: 196 residues
Sequence: SMLDDAKARLRKYDIGGKYSHLPYNKYSVLLPLVAKEGKLHLLFTVRSEKLRRAPGEVCFPGGKRDPTDMDDAATALREAQEEVGLRPHQVEVVCCLVPCLIDTDTLITPFVGLIDHNFQAQPNPAEVKDVFLVPLAYFLHPQVHDQHYVTRLGHRFINHIFEYTNPEDGVTYQIKGMTANLAVLVAFIILEKKPT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1859
R free: 0.2144
Average B factor: 39.652
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K
Matthews coefficient: 4.35
Solvent content (%): 71.75
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: 2019-03-27
Structure of CO2 released holo-form of human carbonic anhydrase II with 3 min warming (PDB entry 5DSK)
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): 1.3
R work: 0.11039
R free: 0.14422
Average B factor: 16.096
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate
100 mM TrisHCl pH 7.8
Matthews coefficient: 2.08
Solvent content (%): 40.85
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: 2016-05-04