3LCD - chain A (model A) | Colony stimulating factor 1 receptor
Structure information
| PDB: | 3LCD |
| PubMed: | 20137931 |
| Release date: | 2010-03-02 |
| Resolution: | 2.5 Å |
| Kinase: | CSF1R (FMS) |
| Family: | PDGFR |
| Group: | TK |
| Species: | HUMAN |
| Quality Score: | 9.4 |
| Missing Residues: | 0 |
| Missing Atoms: | 6 |
| DFG conformation: | in |
| αC-helix conformation: | in |
| Salt bridge KIII.17 and EαC.24: | Yes (3Å) |
| ASP rotation (xDFG.81) : | 341° |
| PHE rotation (xDFG.82) : | 6° |
| Activation loop position: | -3.3Å |
| αC-helix position: | 18.8Å |
| G-rich loop angle: | 60.4° |
| G-rich loop distance: | 18.5Å |
| G-rich loop rotation: | 49.1° |
Other models from this PDB:
2D & 3D views
Binding pocket waters
The following waters were found in the defined clusters:
I1
H-bond ligand
H-bond protein
I4
H-bond protein
I5
H-bond protein
I6
H-bond ligand
H-bond protein
Binding pocket sequence
| Uniprot | KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITEYCCYGDLLNFLRRFLASKNCIHRDVAARNVLLIGDFGLA |
| Structure: | KTLGAGAFGKVVEVAVKMLALMSELKIMSHLGENIVNLLGALVITEYCCYGDLLNFLRRFLASKNCIHRDVAARNVLLIGDFGLA |
Modified residues
No modified residues identified.
Orthosteric ligand
Ligand HET-code: BDY
Ligand Name: N~3~-(2,6-dichlorobenzyl)-5-(4-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}phenyl)pyrazine-2,3-diamine
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- LABELS
- KLIFS residue #
- Amino Acid
- None
- COLORS
- Interaction types
- KLIFS (all res.)
- KLIFS (interacting res.)
- None
- OTHER
- Show/hide non-interacting res.
- En/disable resizing interacting res.
This ligand targets the following (sub)pockets:
| Main pockets | |
|---|---|
| Front | |
| Gate | |
| Back | |
| Subpockets | |
|---|---|
| FP-I | |
| FP-II | |
| BP-I-A | |
| BP-I-B | |
| BP-II-in | |
| BP-II-A-in | |
| BP-II-B-in | |
| BP-II-out | |
| BP-II-B | |
| BP-III | |
| BP-IV | |
| BP-V | |
Kinase-ligand interactions
■ Hydrophobic ♦ Aromatic face-to-face ♦ Aromatic face-to-edge ▲ H-bond donor ▲ H-bond acceptor ● Ionic positive ● Ionic negative
| I | g.l | II | III | αC | |||||||||||||||
| 1 K 586 | 2 T 587 | 3 L 588 | 4 G 589 | 5 A 590 | 6 G 591 | 7 A 592 | 8 F 593 | 9 G 594 | 10 K 595 | 11 V 596 | 12 V 597 | 13 E 598 | 14 V 613 | 15 A 614 | 16 V 615 | 17 K 616 | 18 M 617 | 19 L 618 | 20 A 629 |
| ■ | ■ | ■ | ■ | ■ | |||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 L 630 | 22 M 631 | 23 S 632 | 24 E 633 | 25 L 634 | 26 K 635 | 27 I 636 | 28 M 637 | 29 S 638 | 30 H 639 | 31 L 640 | 32 G 641 | 33 E 644 | 34 N 645 | 35 I 646 | 36 V 647 | 37 N 648 | 38 L 649 | 39 L 650 | 40 G 651 |
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 A 652 | 42 L 660 | 43 V 661 | 44 I 662 | 45 T 663 | 46 E 664 | 47 Y 665 | 48 C 666 | 49 C 667 | 50 Y 668 | 51 G 669 | 52 D 670 | 53 L 671 | 54 L 672 | 55 N 673 | 56 F 674 | 57 L 675 | 58 R 676 | 59 R 677 | 60 F 768 |
| ▲ | ■♦♦ | ■▲ | ■ | ■ | |||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 L 769 | 62 A 770 | 63 S 771 | 64 K 772 | 65 N 773 | 66 C 774 | 67 I 775 | 68 H 776 | 69 R 777 | 70 D 778 | 71 V 779 | 72 A 780 | 73 A 781 | 74 R 782 | 75 N 783 | 76 V 784 | 77 L 785 | 78 L 786 | 79 I 794 | 80 G 795 |
| ■ | ■ | ■ | ■ | ||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 796 | 82 F 797 | 83 G 798 | 84 L 799 | 85 A 800 | |||||||||||||||
| ■ | |||||||||||||||||||
Binding affinities
Ligand not found in ChEMBL.