9HU8: Kalirin/Rac1

Crystal structure of Kalirin/Rac1 in complex with MC-278. Determined by X-ray diffraction at 1.48 Å resolution. Released 14 Jan 2026.

Method: X-ray diffraction
Resolution: 1.48 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 2
Atoms: 3,013
Mol. weight: 41.31 kDa
Ligands: A1IXV
Released: 14 Jan 2026

Explore 9HU8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HU8 contains 26 α-helices and 6 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.

Chain A: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
α-helix	12-14	3
α-helix	16-25	10
β-strand	40-42	3	1
β-strand	53-56	4	1
α-helix	68-71	4
β-strand	77-83	7	1
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	1
α-helix	117-119	3
α-helix	123-131	9
α-helix	136-138	3
α-helix	139-149	11
β-strand	153-156	4	1
α-helix	165-174	10

Chain B: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	1233-1255	23
α-helix	1256-1260	5
α-helix	1261-1264	4
α-helix	1278-1282	5
α-helix	1285-1291	7
α-helix	1292-1296	5
α-helix	1297-1302	6
α-helix	1307-1309	3
α-helix	1311-1316	6
α-helix	1318-1322	5
α-helix	1323-1337	15
α-helix	1338-1342	5
α-helix	1345-1353	9
α-helix	1359-1381	23
α-helix	1389-1407	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related C3 botulinum toxin substrate 1	A	protein	178	Homo sapiens	P63000 (AlphaFold model)
Kalirin	B	protein	182	Rattus norvegicus	P97924 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9HU8_1 Ras-related C3 botulinum toxin substrate 1 (chains A)
SMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTA
GQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDL
RDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVL

Sequence of entity 2 (B), FASTA

>9HU8_2 Kalirin (chains B)
SMRKKEFIMAELLQTEKAYVRDLHECLETYLWEMTSGVEEIPPGILNKEHIIFGNIQEIY
DFHNNIFLKELEKYEQLPEDVGHCFVTWADKFQMYVTYCKNKPDSNQLILEHAGTFFDEI
QQRHGLANSISSYLIKPVQRVTKYQLLLKELLTCCEEGKGELKDGLEVMLSVPKKANDAM
HV

Ligands and cofactors

ID	Name	Formula	Copies
A1IXV	2-chloranyl-~{N}-(2-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-1,8-naphthyridin-4-y…	C10 H12 Cl N3 O2	1

Primary citation

Discovery of inhibitor fragments of the Kalirin/Rac1 Rho GEF/GTPase. Gray, J.L., Callens, M.C., von Delft, F. et al. To be published.

Other PDB entries of the same protein (UniProt P63000 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RFF 1.25 Å, Crystal Structure of Human Rac1 Fused with the Scaffold Protein POSH (residues 319-371)
9IFK 1.34 Å, Crystal structure of Kalirin/Rac1 in complex with DK-2
1MH1 1.38 Å, Small G-protein
2WKQ 1.6 Å, Structure of a photoactivatable Rac1 containing the Lov2 C450A Mutant
6X1G 1.6 Å, Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in…
5O33 1.64 Å, A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1
9IG1 1.65 Å, Crystal structure of Kalirin/Rac1 in complex with DK-652
9I1L 1.68 Å, Crystal structure of Kalirin/Rac1 in complex with RS-009
8I5V 1.73 Å, DOCK10 mutant L1903Y complexed with Rac1
1RYF 1.75 Å, Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
1RYH 1.75 Å, Alternative Splicing of Rac1 Generates Rac1b, a Self-activating GTPase
9TJY 1.77 Å, Crystal Structure of the Human Oncogenic Splice Variant Rac1b Fused with the Scaffold…

Browse structure collections

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