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- PDB-3q2g: Adamts1 in complex with a novel N-hydroxyformamide inhibitors -

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Basic information

Entry
Database: PDB / ID: 3q2g
TitleAdamts1 in complex with a novel N-hydroxyformamide inhibitors
ComponentsA disintegrin and metalloproteinase with thrombospondin motifs 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Adamts1 Zn-Metalloprotease / disintegrin / metalloproteinase / thrombospondin motifs / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / positive regulation of vascular associated smooth muscle cell migration / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix ...Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / positive regulation of vascular associated smooth muscle cell migration / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / negative regulation of angiogenesis / extracellular matrix organization / extracellular matrix / kidney development / integrin-mediated signaling pathway / metalloendopeptidase activity / metallopeptidase activity / heparin binding / cytoplasmic vesicle / negative regulation of cell population proliferation / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Peptidase M12B, ADAM-TS1 / YefM-like fold - #60 / Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain ...Peptidase M12B, ADAM-TS1 / YefM-like fold - #60 / Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / YefM-like fold / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / Chem-QGF / A disintegrin and metalloproteinase with thrombospondin motifs 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGerhardt, S. / Hargreaves, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: The design and synthesis of novel N-hydroxyformamide inhibitors of ADAM-TS4 for the treatment of osteoarthritis
Authors: De Savi, C. / Pape, A. / Cumming, J.G. / Ting, A. / Smith, P.D. / Burrows, J.N. / Mills, M. / Davies, C. / Lamont, S. / Milne, D. / Cook, C. / Moore, P. / Sawyer, Y. / Gerhardt, S.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A disintegrin and metalloproteinase with thrombospondin motifs 1
B: A disintegrin and metalloproteinase with thrombospondin motifs 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,84627
Polymers65,1572
Non-polymers2,68925
Water2,540141
1
A: A disintegrin and metalloproteinase with thrombospondin motifs 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,11516
Polymers32,5791
Non-polymers1,53715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A disintegrin and metalloproteinase with thrombospondin motifs 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,73111
Polymers32,5791
Non-polymers1,15210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.309, 63.419, 114.912
Angle α, β, γ (deg.)90.00, 89.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A4 - 169
2115B4 - 169
1215A175 - 181
2215B175 - 181
1315A185 - 248
2315B185 - 248
1415A253 - 261
2415B253 - 261
1515A266 - 299
2515B266 - 299

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein A disintegrin and metalloproteinase with thrombospondin motifs 1 / ADAMTS-1


Mass: 32578.551 Da / Num. of mol.: 2 / Fragment: residues in UNP 256-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAMTS1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9UHI8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 7 types, 166 molecules

#2: Chemical ChemComp-QGF / N-[(2S,4S)-1-({4-[(2,4-dichlorobenzyl)oxy]piperidin-1-yl}sulfonyl)-4-(5-fluoropyrimidin-2-yl)-2-methylpentan-2-yl]-N-hydroxyformamide


Mass: 563.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29Cl2FN4O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.13 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorDate: Dec 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→114.71 Å / Num. obs: 31938 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.3 % / % possible all: 96.1

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JIH

2jih


Resolution: 2.3→114.71 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.114 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.24 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26068 1615 5.1 %RANDOM
Rwork0.20804 ---
obs0.21071 30306 96.47 %-
all-31307 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.3 Å2 / Biso mean: 37.664 Å2 / Biso min: 10.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å21.19 Å2
2--2.51 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→114.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4336 0 95 141 4572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214530
X-RAY DIFFRACTIONr_bond_other_d0.0010.023778
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9526164
X-RAY DIFFRACTIONr_angle_other_deg0.838864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58324.925201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01415713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8281515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
X-RAY DIFFRACTIONr_nbd_refined0.2040.21056
X-RAY DIFFRACTIONr_nbd_other0.1770.23702
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22192
X-RAY DIFFRACTIONr_nbtor_other0.0840.22418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2202
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_metal_ion_refined0.150.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0450.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5271.52805
X-RAY DIFFRACTIONr_mcbond_other0.1071.51139
X-RAY DIFFRACTIONr_mcangle_it0.99324515
X-RAY DIFFRACTIONr_scbond_it1.42231791
X-RAY DIFFRACTIONr_scangle_it2.2954.51649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1635medium positional0.510.5
2362loose positional0.785
1635medium thermal0.552
2362loose thermal1.0110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 112 -
Rwork0.239 2208 -
all-2320 -
obs--95 %
Refinement TLS params.Method: refined / Origin x: 24.3928 Å / Origin y: -0.1394 Å / Origin z: 30.302 Å
111213212223313233
T-0.1147 Å20.0098 Å20 Å2--0.098 Å20.0167 Å2---0.0765 Å2
L0.6703 °20.0809 °20.1192 °2-0.7103 °20.6314 °2--1.8247 °2
S-0.0054 Å °-0.1077 Å °0.0303 Å °-0.0184 Å °-0.0073 Å °0.0094 Å °-0.0436 Å °-0.0259 Å °0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 299
2X-RAY DIFFRACTION1B4 - 300

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