4RDD: Co-crystal structure of SHP2

Co-crystal structure of SHP2 in complex with a Cefsulodin derivative. Determined by X-ray diffraction at 1.6 Å resolution. Released 1 Jul 2015.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,547
Mol. weight: 32.66 kDa
Ligands: 3LU
Released: 1 Jul 2015

Explore 4RDD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RDD contains 11 α-helices and 11 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	266-269	4
α-helix	271-276	6
β-strand	289-291	3	1
β-strand	304-310	7	1
β-strand	327-330	4	1
α-helix	331-334	4
α-helix	335-337	3
α-helix	338-348	11
β-strand	352-355	4	1
β-strand	360-361	2	2
β-strand	364-365	2	2
α-helix	372-373	2
β-strand	377-380	4	1
β-strand	383-392	10	1
β-strand	396-405	10	1
β-strand	413-420	8	1
α-helix	433-448	16
α-helix	454	1
β-strand	455-458	4	1
α-helix	464-482	19
α-helix	490-498	9
α-helix	508-526	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosine-protein phosphatase non-receptor type 11	A	protein	275	Homo sapiens	Q06124 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4RDD_1 Tyrosine-protein phosphatase non-receptor type 11 (chains A)
LYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNS
KPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYG
VMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEE
VHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQR
SGMVQTEAQYRFIYMAVQHYIETLQRRLEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
3LU	1-({(2R)-4-carboxy-2-[(R)-carboxy{[(2R)-2-phenyl-2-sulfoacetyl]amino}methyl]-3,…	C21 H22 N3 O8 S2	1

Primary citation

Exploring the Existing Drug Space for Novel pTyr Mimetic and SHP2 Inhibitors. He, R., Yu, Z.H., Zhang, R.Y. et al. ACS Med Chem Lett (2015) 6:782-786. DOI 10.1021/acsmedchemlett.5b00118 · PubMed

Other PDB entries of the same protein (UniProt Q06124 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9EIK 1.25 Å, Crystal structure of N-SH2 domain of SHP2 with T42A mutation bound to GAB1 tyrosine…
3ZM1 1.4 Å, Catalytic domain of human SHP2
4JMG 1.4 Å, Crystal structure of the synthetic protein in complex with pY peptide
7PPM 1.48 Å, SHP2 catalytic domain in complex with IRS1 (889-901) phosphopeptide (pSer-892, pTyr-896)
3ZM0 1.5 Å, Catalytic domain of human SHP2
3ZM2 1.5 Å, Catalytic domain of human SHP2
3ZM3 1.5 Å, Catalytic domain of human SHP2
7PPL 1.53 Å, SHP2 catalytic domain in complex with IRS1 (625-639) phosphopeptide (pTyr-632, pSer-636)
9EIC 1.58 Å, Crystal structure of unbound N-SH2 domain of SHP2 with T42A mutation
9EHD 1.59 Å, Crystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine phosphorylated peptide…
3B7O 1.6 Å, Crystal structure of the human tyrosine phosphatase SHP2 (PTPN11) with an accessible…
5EHR 1.7 Å, Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP099

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