From my current experience which is quite limited as I am currently an applicant, it is difficult to predict reliably whether or not having just one first author publication will or will not hurt you. I have learned from this process that each program has subtle differences it is looking for from its prospective resident candidates. I am an MD\PhD with three non RadOnc first author pubs from my PhD, I have good step scores and good grades as well as other RadOnc projects\pubs. What I have found is that having a number of first author pubs from my PhD is simply not enough to get the Harvards, Michigans, Yales etc. From speaking with other MD\PhDs who did get those places, our scores were similar but their pubs were RadOnc, MedOnc or in high impact factor journals. That is what those places are looking for from an MD\PhD. Now with this aside, I have some really good interviews at places just below these giants. So having a PhD will NOT hurt you. I recommend just applying very broadly and you will be surprised at the places you receive interviews from, assuming grades and Step are good.