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Found 1 Document (0.365 seconds)

BMRB: 34165

5OJT

Structure-Activity Relationships and Biological Characterization of a Novel, Potent and Serum Stable C-X-C chemokine receptor type 4 (CXCR4) Antagonist

Authors

Brancaccio, D., Carotenuto, A.

Assembly

ACE-ARG-ALA-(D)CYS-ARG-BNA-HIS-PEN

Entity

1. ACE-ARG-ALA-(D)CYS-ARG-BNA-HIS-PEN (polymer, Thiol state: not present), 8 monomers, 996.2122 Da Detail

XRAXRXHX

Formula weight

996.2122 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 50.0 %, Completeness: 100.0 %, Completeness (bb): 100.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	100.0 % (27 of 27)	100.0 % (27 of 27)
Backbone	100.0 % (8 of 8)	100.0 % (8 of 8)
Sidechain	100.0 % (19 of 19)	100.0 % (19 of 19)
Aromatic	100.0 % (2 of 2)	100.0 % (2 of 2)
Methyl	100.0 % (1 of 1)	100.0 % (1 of 1)

1. entity 1

XRAXRXHX

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.5, Details 2 mM NA Peptide, 200 mM [U-99% 2H] SDS, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Peptide	natural abundance		2 mM
2	SDS	[U-99% 2H]		200 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 5OJT, Strand ID: A Detail

Release date

2017-11-12

Citation

Structure-Activity Relationships and Biological Characterization of a Novel, Potent, and Serum Stable C-X-C Chemokine Receptor Type 4 (CXCR4) Antagonist
Di Maro, S., Di Leva, F.S., Trotta, A.M., Brancaccio, D., Portella, L., Aurilio, M., Tomassi, S., Messere, A., Sementa, D., Lastoria, S., Carotenuto, A., Novellino, E., Scala, S., Marinelli, L.
J. Med. Chem. (2017), 60, 9641-9652, PubMed 29125295 , DOI 10.1021/acs.jmedchem.7b01062 , Abstract

Experiments performed 3 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34165_5ojt.nef
Input source #2: Coordindates	5ojt.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:4:DCY:SG	A:8:LE1:SG	unknown	unknown	2.013

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:1:ACE:C	1:2:ARG:N	unknown	unknown	n/a
1:3:ALA:C	1:4:DCY:N	unknown	unknown	n/a
1:4:DCY:C	1:5:ARG:N	unknown	unknown	n/a
1:5:ARG:C	1:6:NAL:N	unknown	unknown	n/a
1:6:NAL:C	1:7:HIS:N	unknown	unknown	n/a
1:7:HIS:C	1:8:LE1:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	1	ACE	ACETYL GROUP	Assigned chemical shifts, Coordinates
A	4	DCY	D-CYSTEINE	Assigned chemical shifts, Coordinates
A	6	NAL	BETA-(2-NAPHTHYL)-ALANINE	Assigned chemical shifts, Coordinates
A	8	LE1	3-sulfanyl-L-valine	Assigned chemical shifts, Coordinates

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------
XRAXRXHX
||||||||
XRAXRXHX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	8	0	0	100.0

Content subtype: combined_34165_5ojt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	7		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Error	44		100.0 (chain: A, length: 8)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	42 (1)	noe	50.0 (chain: A, length: 8)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 8, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 44
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID
4	DCY
6	NAL
8	LE1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	29	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	9	9	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	20	20	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 8, Sequence coverage: 50.0%
- Total number of restraints: 42
- Weight of restraints: 1.0 (42)
- Potential type of restraints: upper-bound-parabolic (42)
- Range of distance target values: 2.89, 6.53 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords CXCR4, PEPTIDE BINDING PROTEIN

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Found 1 Document (0.365 seconds)

BMRB: 34165

Sample

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail