Crystal Structure of Ephrin B4 (EphB4) Receptor Protein Kinase with an isomer of NVP-BHG712. Determined by X-ray diffraction at 1.24 Å resolution. Released 8 Aug 2018.
Explore 6FNJ in 3D Show helices and sheets RCSB PDB PDBe
6FNJ contains 35 α-helices and 24 β-strands across 2 chains. 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 609 | 1 | 1 |
| α-helix | 612-614 | 3 | |
| β-strand | 615-623 | 9 | 1 |
| β-strand | 628-634 | 7 | 1 |
| α-helix | 640-641 | 2 | |
| β-strand | 642-649 | 8 | 1 |
| α-helix | 655-668 | 14 | |
| β-strand | 676 | 1 | 2 |
| α-helix | 677-678 | 2 | |
| β-strand | 679-683 | 5 | 1 |
| β-strand | 689-694 | 6 | 1 |
| β-strand | 700 | 1 | 2 |
| α-helix | 701-707 | 7 | |
| α-helix | 714-733 | 20 | |
| α-helix | 743-745 | 3 | |
| β-strand | 746-748 | 3 | 2 |
| β-strand | 754-756 | 3 | 2 |
| α-helix | 784-786 | 3 | |
| α-helix | 789-794 | 6 | |
| α-helix | 799-814 | 16 | |
| α-helix | 818-819 | 2 | |
| α-helix | 826-834 | 9 | |
| α-helix | 839-842 | 4 | |
| β-strand | 846 | 1 | 3 |
| α-helix | 847-856 | 10 | |
| α-helix | 861-863 | 3 | |
| α-helix | 865-866 | 2 | |
| α-helix | 867-879 | 13 | |
| α-helix | 881-884 | 4 | |
| β-strand | 887 | 1 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 609 | 1 | 4 |
| α-helix | 612-614 | 3 | |
| β-strand | 615-623 | 9 | 4 |
| β-strand | 628-634 | 7 | 4 |
| β-strand | 642-649 | 8 | 4 |
| α-helix | 655-669 | 15 | |
| β-strand | 676 | 1 | 5 |
| α-helix | 677-678 | 2 | |
| β-strand | 679-683 | 5 | 4 |
| β-strand | 689-694 | 6 | 4 |
| β-strand | 700 | 1 | 5 |
| α-helix | 701-707 | 7 | |
| α-helix | 714-733 | 20 | |
| α-helix | 743-745 | 3 | |
| β-strand | 746-748 | 3 | 5 |
| β-strand | 754-756 | 3 | 5 |
| α-helix | 784-786 | 3 | |
| α-helix | 789-794 | 6 | |
| α-helix | 799-814 | 16 | |
| α-helix | 818-819 | 2 | |
| α-helix | 826-834 | 9 | |
| α-helix | 839-842 | 4 | |
| β-strand | 846 | 1 | 6 |
| α-helix | 847-856 | 10 | |
| α-helix | 861-863 | 3 | |
| α-helix | 865-866 | 2 | |
| α-helix | 867-879 | 13 | |
| α-helix | 881-885 | 5 | |
| β-strand | 887 | 1 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Ephrin type-B receptor 4 | A, B | protein | 297 | Homo sapiens | P54760 (AlphaFold model) |
>6FNJ_1 Ephrin type-B receptor 4 (chains A, B) GMDPNEAVREFAKEIDVSYVKIEEVIGAGEFGEVCRGRLKAPGKKESCVAIKTLKGGYTE RQRREFLSEASIMGQFEHPNIIRLEGVVTNSMPVMILTEFMENGALDSFLRLNDGQFTVI QLVGMLRGIASGMRYLAEMSYVHRDLAARNILVNSNLVCKVSDFGLSRFLEENSSDPTET SSLGGKIPIRWTAPEAIAFRKFTSASDVWSYGIVMWEVMSFGERPYWDMSNQDVINAIEQ DYRLPPPPDCPTSLHQLMLDCWQKDRNARPRFPQIVSALDKMIRNPASLKIVARENG
| ID | Name | Formula | Copies |
|---|---|---|---|
| DWT | 4-methyl-3-[(2-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-yl)amino]-~{N}-… | C26 H20 F3 N7 O | 2 |
Water and common crystallization additives (EDO) are not listed.
NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. Troster, A., Heinzlmeir, S., Berger, B.T. et al. ChemMedChem (2018) 13:1629-1633. DOI 10.1002/cmdc.201800398 · PubMed
Other PDB entries of the same protein (UniProt P54760 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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