satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal Structure of Human DNA Polymerase Eta Inserting dATP Opposite O4-Methylhymidine (PDB entry 5DLF)
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): 1.97
R work: 0.16368
R free: 0.21707
Average B factor: 23.758
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M MES pH 5.5, 5mM magnesium chloride, 18% PEG 2000 MME
Matthews coefficient: 2.13
Solvent content (%): 42.15
Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTP)
Ligand formula: C10 H16 N5 O12 P3
Ligand molecular weight: 491.182
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N
Ligand InChI: InChI=1S/C10H16N5O12P3/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(25-7)2-24-29(20,21)27-30(22,23)26-28(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H,22,23)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1
Release date: 2016-08-10
Crystal structure of human paired immunoglobulin-like type 2 receptor alpha with synthesized glycopeptide I (PDB entry 5XOF)
Macromolecule: Paired immunoglobulin-like type 2 receptor alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 120 residues
Sequence: MLYGVTQPKHLSASMGGSVEIPFSFYYPWELATAPDVRISWRRGHFHGQSFYSTRPPSIHKDYVNRLFLNWTEGQKSGFLRISNLQKQDQSVYFCRVELDTRSSGRQQWQSIEGTKLSIT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.963
R work: 0.2145
R free: 0.2692
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M Tris-HCl pH8.5, 25% (w/v) PEG 6000
Matthews coefficient: 2.2
Solvent content (%): 44.18
Release date: 2017-10-25
Aspartyl/Asparaginyl beta-hydroxylase (AspH) H679A in complex with Factor X peptide fragment (39mer-4Ser) (PDB entry 6Q9I)
Macromolecule: Coagulation factor X
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.6
Sequence length: 39 residues
Sequence: DGDQSETSPSQNQGKCKDGLGEYTCTSLEGFEGKNSELF
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.852
R work: 0.202
R free: 0.2233
Average B factor: 59
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M sodium formate, 20 % w/v PEG 3350
Matthews coefficient: 2.7
Solvent content (%): 54.5
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: 2020-01-15
Crystal structure of DARPin-DARPin rigid fusion, variant DD_D12_10_47 in complex JNK1a1 and JIP1 peptide (PDB entry 6F5E)
Macromolecule: DD_D12_10_47
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 325 residues
Sequence: MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILLANGADVNTADETGFTPLHLAAWEGHLGIVEVLLKNGADVNANDERGHTPLHLAAYTGHLEIVEVLLKNGAGVNATDVIGTAPLHLAAMWGHLEIVEVLLKNGADVNAQDKFGKTPYDLATDNGNQWIAELLKRAALRRKLLEAARAGHRDEVEDLIKNGADVNAIDAMGLTPLHLAAMRGHLEIVEVLLKYGADVNAEDYYGTTPLRLAAYIGHLEIVEVLLKYGADVNAYDISGTTPLHLAAVLGHLEIVEVLLKYGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.2005
R free: 0.2261
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.8
Crystallization temperature (K): 277
Crystal growth procedure: PEG 10000 3% w/v 
Hepes 0.1 M, pH 6.8 
Additives (0.033% w/v)
1,5-Naphthalene-
disulfonic acid disodium salt 
2,5-Pyridinedicarboxylic acid 
3,5-Dinitrosalicylic acid
Matthews coefficient: 3.55
Solvent content (%): 65.4
Release date: 2017-12-13
Carbonic Anhydrase II complexed with benzene sulfonamide MB11-707A (PDB entry 6OUE)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 257 residues
Sequence: HWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.415
R work: 0.1673
R free: 0.1947
Average B factor: 20.5845
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 298
Crystal growth procedure: 1.6M sodium citrate, 50mM Tris HCl, pH 7.8
Matthews coefficient: 2.06
Solvent content (%): 40.4
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-05-06
Crystal structure of human PCAF bromodomain in complex with fragment ZB1916 (fragment 10) (PDB entry 5FE6)
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): 1.77
R work: 0.17941
R free: 0.21248
Average B factor: 45.06
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: 3.38
Solvent content (%): 63.6
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: 2016-01-13
PAC-FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit discovery (PDB entry 8AHI)
Macromolecule: Serine/threonine-protein kinase PAK 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 297 residues
Sequence: GPLGSSHEQFRAALQAVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFNEVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVLQALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPELISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSLKGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQNRTR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.69
R work: 0.1552
R free: 0.2489
Average B factor: 29.915
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.8M Na/K tartrate
0.1M Tris pH 8.5
Matthews coefficient: 2.52
Solvent content (%): 50.72
Ligand: ~{N}-methyl-1,3-benzothiazole-6-carboxamide (M56)
Ligand formula: C9 H8 N2 O S
Ligand molecular weight: 192.238
Ligand SMILES: CNC(=O)c1ccc2c(c1)scn2
Ligand InChI: InChI=1S/C9H8N2OS/c1-10-9(12)6-2-3-7-8(4-6)13-5-11-7/h2-5H,1H3,(H,10,12)
Release date: 2022-09-14
Crystal Structure of human cyclic GMP-AMP synthase in complex with 5-[3-[[(5-bromo-2-hydroxybenzoyl)amino]methyl]phenyl]-2-methylpyrazole-3-carboxylic acid (PDB entry 7FU1)
Macromolecule: Cyclic GMP-AMP synthase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.86
Sequence length: 362 residues
Sequence: GASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.074
R work: 0.2225
R free: 0.2757
Average B factor: 72.7849
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10-12 mg/mL protein in 25 mM Tris/HCl pH7.5, 500mM NaCl, 2mM TCEP, supplemented with 10x molar excess of ligand and, if needed, with 10 mM MgCl2 and 5mM ATP, then mixed 1:1 with reservoir of the Procomplex screen. Several conditions resulted in crystals.
Matthews coefficient: 2.59
Solvent content (%): 52.48
Ligand: (3P)-3-{3-[(5-bromo-2-hydroxybenzamido)methyl]phenyl}-1-methyl-1H-pyrazole-5-carboxylic acid (YU2)
Ligand formula: C19 H16 Br N3 O4
Ligand molecular weight: 430.252
Ligand SMILES: Cn1c(cc(n1)c2cccc(c2)CNC(=O)c3cc(ccc3O)Br)C(=O)O
Ligand InChI: InChI=1S/C19H16BrN3O4/c1-23-16(19(26)27)9-15(22-23)12-4-2-3-11(7-12)10-21-18(25)14-8-13(20)5-6-17(14)24/h2-9,24H,10H2,1H3,(H,21,25)(H,26,27)
Release date: 2024-02-21
BMP1 complexed with a reverse hydroxymate - compound 22 (PDB entry 6BSL)
Macromolecule: Bone morphogenetic protein 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.19
Sequence length: 202 residues
Sequence: XAATSRPERVWPDGVIPFVIGGNFTGSQRAVFRQAMRHWEKHTCVTFLERTDEDSYIVFTYRPCGCCSYVGRRGGGPQAISIGKNCDKFGIVVHELGHVVGFWHEHTRPDRDRHVSIVRENIQPGQEYNFLKMEPQEVESLGETYDFDSIMHYARNTFSRGIFLDTIVPKYEVNGVKPPIGQRTRLSKGDIAQARKLYKCPA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.45
R work: 0.1925
R free: 0.2093
Average B factor: 17.452
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 8-12% PEG3350, 150-200 KSCN, 10mM spermadine
Matthews coefficient: 2.67
Solvent content (%): 53.98
Ligand: THIOCYANATE ION (SCN)
Ligand formula: C N S
Ligand molecular weight: 58.082
Ligand SMILES: C(#N)[S-]
Ligand InChI: InChI=1S/CHNS/c2-1-3/h3H/p-1
Release date: 2018-08-08
Crystal Structure of human phosphodiesterase 10 in complex with 4-[1-methyl-6-[(1-methyl-4-phenylimidazol-2-yl)methoxy]pyrazolo[3,4-d]pyrimidin-4-yl]morpholine (PDB entry 5SGH)
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): 1.97
R work: 0.1766
R free: 0.2196
Average B factor: 37.525
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 (%): 52.78
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 for the complex of human carbonic anhydrase IV and methazolamide (PDB entry 5KU6)
Macromolecule: Carbonic anhydrase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 266 residues
Sequence: AESHWCYEVQAESSNYPCLVPVKWGGNCQKDRQSPINIVTTKAKVDKKLGRFFFSGYDKKQTWTVQNNGHSVMMLLENKASISGGGLPAPYQAKQLHLHWSDLPYKGSEHSLDGEHFAMEMHIVHEKEKGTSRNVKEAQDPEDEIAVLAFLVEAGTQVNEGFQPLVEALSNIPKPEMSTTMAESSLLDLLPKEEKLRHYFRYLGSLTTPTCDEKVVWTVFREPIQLHREQILAFSQKLYYDKEQTVSMKDNVRPLQQLGQRTVIKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.18416
R free: 0.21585
Average B factor: 22.503
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 4.6
Crystallization temperature (K): 277
Crystal growth procedure: 100 mM Na acetate, 200 mM AmSO4 and 23% PEG 4000
Matthews coefficient: 2.5
Solvent content (%): 50.87
Ligand: N-(3-methyl-5-sulfamoyl-1,3,4-thiadiazol-2(3H)-ylidene)acetamide (MZM)
Ligand formula: C5 H8 N4 O3 S2
Ligand molecular weight: 236.272
Ligand SMILES: CC(=O)N=C1N(N=C(S1)S(=O)(=O)N)C
Ligand InChI: InChI=1S/C5H8N4O3S2/c1-3(10)7-4-9(2)8-5(13-4)14(6,11)12/h1-2H3,(H2,6,11,12)/b7-4-
Release date: 2017-07-26
Crystal structure of mouse Plk1-PBD in complex with phosphopeptide from HEF1 (799-809) (PDB entry 5X3S)
Macromolecule: Peptide from Enhancer of filamentation 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 11 residues
Sequence: LHYPSTTALQE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.899
R work: 0.2025
R free: 0.2441
Average B factor: 38.6935
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 291
Crystal growth procedure: 15% PEG 6000, 0.1M sodium citrate
Matthews coefficient: 2.28
Solvent content (%): 46.12
Release date: 2017-12-20
Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC derivatives (PDB entry 6L14)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 289 residues
Sequence: GPHMKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1925
R free: 0.2094
Average B factor: 42.887
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 0.4M potassium sodium tartrate tetrahydrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 3.6
Solvent content (%): 65.87
Ligand: 2-chloranyl-10-[3-[(3~{S})-piperidin-3-yl]propyl]phenoxazine (E2L)
Ligand formula: C20 H23 Cl N2 O
Ligand molecular weight: 342.862
Ligand SMILES: c1ccc2c(c1)N(c3cc(ccc3O2)Cl)CCCC4CCCNC4
Ligand InChI: InChI=1S/C20H23ClN2O/c21-16-9-10-20-18(13-16)23(17-7-1-2-8-19(17)24-20)12-4-6-15-5-3-11-22-14-15/h1-2,7-10,13,15,22H,3-6,11-12,14H2/t15-/m0/s1
Release date: 2020-05-27
Crystal Structure of METTL9-SAH (PDB entry 8GZF)
Macromolecule: Protein-L-histidine N-pros-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1
Sequence length: 266 residues
Sequence: NHQWYVCNREKLCESLQAVFVQSYLDQGTQIFLNNSIEKSGWLFIQLYHSFVSSVFSLFMSRTSINGLLGRGSMFVFSPDQFQRLLKINPDWKTHRLLDLGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGINEWQNTGFQYDVISCLNLLDRCDQPLTLLKDIRSVLEPTRGRVILALVLPFHPYVENVGGKWEKPSEILEIKGQNWEEQVNSLPEVFRKAGFVIEAFTRLPYLCEGDMYNDYYVLDDAVFVLKPV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.1902
R free: 0.2409
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 4% v/v glycerol, 1.8 M NaCl
Matthews coefficient: 3.39
Solvent content (%): 63.7
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2023-05-31
Fusion of Pyk2-FAT domain with Leupaxin LD1 motif, complexed with Leupaxin LD4 peptide (PDB entry 4XEV)
Macromolecule: Fusion protein of Protein-tyrosine kinase 2-beta FAT domain and Leupaxin LD1 motif
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 167 residues
Sequence: GSHMANLDRTDDLVYLNVMELVRAVLELKNELSQLPPEGYVVVVKNVGLTLRKLIGSVDDLLPSLPSSSRTEIEGTQKLLNKDLAELINKMRLAQQNAVTSLSEEAKRQMLTASHTLAVDAKNLLDAVDQAKVLANLAHGGSGGGGGMEELDALLEELERSTLQDSD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0073
R work: 0.2039
R free: 0.2502
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 291.2
Crystal growth procedure: The 4 ul drop contained 2 ul protein/LD4 peptide mixture (20 mM MES pH 6.2, 1 mM protein, and 2 mM peptide) and 2 ul well solution (100 mM MES pH 6.5 and 25 % PEG 3000).
Matthews coefficient: 2.42
Solvent content (%): 49.12
Release date: 2015-12-30
Crystal Structure of human phosphodiesterase 10 in complex with 5,8-dimethyl-2-[(E)-2-[2-methyl-5-(1H-pyrazol-4-yl)-1,2,4-triazol-3-yl]ethenyl]-[1,2,4]triazolo[1,5-a]pyrazine (PDB entry 5SFY)
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): 2.08
R work: 0.1823
R free: 0.2249
Average B factor: 40.407
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: 2.62
Solvent content (%): 53.01
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: 2022-10-12
Novel pyrrole carboxamide inhibitors of JAK2 as potential treatment of myeloproliferative disorders (PDB entry 5AEP)
Macromolecule: TYROSINE-PROTEIN KINASE JAK2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 298 residues
Sequence: AFEDRDPTQFEERHLKFLQQLGKGNFGSVEMCRYDPLQDNTGEVVAVKKLQHSTEEHLRDFEREIEILKSLQHDNIVKYKGVCYSAGRRNLKLIMEYLPYGSLRDYLQKHKERIDHIKLLQYTSQICKGMEYLGTKRYIHRDLATRNILVENENRVKIGDFGLTKVLPQDKEYYKVKEPGESPIFWYAPESLTESKFSVASDVWSFGVVLYELFTYIEKSKSPPAEFMRMIGNDKQGQMIVFHLIELLKNNGRLPRPDGCPDEIYMIMTECWNNNVNQRPSFRDLALRVDQIRDNMAG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.17114
R free: 0.21335
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 1.5-2.2 M SODIUM MALONATE PH 7, HANGING DROP AT 20 DEGREES CELSIUS
Matthews coefficient: 2.29
Solvent content (%): 46.32
Ligand: 1-(5-chloro-2-methylphenyl)-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yl)-1H-pyrrole-2-carboxamide (QUP)
Ligand formula: C18 H14 Cl N5 O
Ligand molecular weight: 351.79
Ligand SMILES: Cc1ccc(cc1n2cc(cc2C(=O)N)c3c4cccn4ncn3)Cl
Ligand InChI: InChI=1S/C18H14ClN5O/c1-11-4-5-13(19)8-15(11)23-9-12(7-16(23)18(20)25)17-14-3-2-6-24(14)22-10-21-17/h2-10H,1H3,(H2,20,25)
Release date: 2015-04-29
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z939944666 (PDB entry 5RXH)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.42
R work: 0.1795
R free: 0.2034
Average B factor: 17.038
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.04
Solvent content (%): 39.85
Ligand: 3-fluoro-4-(piperazin-1-yl)benzonitrile (WK7)
Ligand formula: C11 H12 F N3
Ligand molecular weight: 205.231
Ligand SMILES: c1cc(c(cc1C#N)F)N2CCNCC2
Ligand InChI: InChI=1S/C11H12FN3/c12-10-7-9(8-13)1-2-11(10)15-5-3-14-4-6-15/h1-2,7,14H,3-6H2
Release date: 2020-11-11
Crystal structure of Ser/Thr kinase Pim1 in complex with Mitoxantrone derivatives (PDB entry 4RC2)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 289 residues
Sequence: GPHMKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPSK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.096
R work: 0.20803
R free: 0.24559
Average B factor: 41.426
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.4 M potassium sodium tartrate tetrahydrate, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Matthews coefficient: 3.36
Solvent content (%): 63.44
Ligand: 1-amino-5,8-dihydroxy-4-({2-[(2-hydroxyethyl)amino]ethyl}amino)anthracene-9,10-dione (3O8)
Ligand formula: C18 H19 N3 O5
Ligand molecular weight: 357.361
Ligand SMILES: c1cc(c2c(c1N)C(=O)c3c(ccc(c3C2=O)O)O)NCCNCCO
Ligand InChI: InChI=1S/C18H19N3O5/c19-9-1-2-10(21-6-5-20-7-8-22)14-13(9)17(25)15-11(23)3-4-12(24)16(15)18(14)26/h1-4,20-24H,5-8,19H2
Release date: 2015-03-18