What is Sobek's place in the Egyptian pantheon?
Sobek is a god that has been worshipped throughout all the Egyptian, from the Old Kingdom up to the Ptolemy time. His name in Egyptian is SBK [notice the hieroglyphs S (reed) + B (foot) + K (basket) + determinative crocodile (optional) + God sign], it is not known the origin. let's also say the term ruler in old Egyptian was written crocodile crocodile falcon [ity in old egyptian] making relatively clear that Sobek is not a second zone god, it is a direct embodiment of the power of the pharaoh as Horus. Let's see what the Egyptian said:
The Old Kingdom is the time of the Pyramids (forget once and for all those Hollywoodian movies depicting Ramses building Pyramids with tons of slaves). The Pyramid Texts are a series of incantations found in the pyramids, in hieroglyphs you can find on the internet some translations, and even hiero yphs, if you can decipher them [the institute of Chicago provides a whole bunch of them]. Here are some texts:
Tomb of unis/Unas, 212: Unis has looked at you like Horus looks at Isis, Unis has looked at you like Kas-Assigner looks at Selket, Unis has looked at you like Sobek looks at Neith, Unis has looked at you like Seth looks at the two reconciled gods.
So clearly Neith is linked as Sobek mother. Later:
Tomb of Unis 222: Unis has come here in advance of the flood’s immersion: Unis is Sobek, green of plumage, 86 with alert face and raised fore, the splashing one who came from the thigh and tail of the great goddess in the sunlight.
Sobek is green of plumage (An obvious reference to the fat crocodile are green and to the Nile fertile covered with vegetation [plumage]). note that green is Egyptian is wAD or wadj, which is used also for vigorous, valiant, energetic, etc.
Tomb of unis 222 Unis has appeared as Sobek, Neith’s son. Unis will eat with his mouth, Unis will urinate and Unis will copulate with his penis. Unis is lord of semen, who takes women from their husbands to the place Unis likes according to his heart’s fancy.
Here we see once again Sobek referred quite clearly as Neith's son and linked with fertility (male one) and who takes women from their husbands. Which is so clearly an attribute of Sobek. Here is another Sobek thing:
Tomb of Pepi 478: My father has inherited from Horus as Horus in Seal-ring, Seth in the Ennead, Sobek in [Shedit].
So Sobek is not from the Ennead but related to Shedit. What is Shedit? Shedit or Shedet is also called Faiyum or in Greek Krokodilopolis or in Roman Arsinoe, it is and still is an Egyptian city.
Tomb of Pepi 523: His face is that of a jackal, his middle is that of Qebehut: he will give judgment as Sobek in Shedit and as Anubis in Takhbit
Takhbit is a site associated with Seth, we don't know where it was situated.
So Sobek is known during the old Kingdom, obviously as the son of Neith, linked to the crocodiles, the vegetation, the marsh, the semen, the fertility. He is NOT at all from the Enead. And we can clearly see is nature as quite sexual (consider he takes the wife out of the husband...) and not cool... As the crocodile btw.
The Middle Kingdom is arguably less known by people. No more pyramids, and not yet the sumptuous building from the New Kingdom... We have lots of texts written in sarcophagus known as "Coffin Texts". Those texts are based on the Pyramid Texts and were written inside the sarcophagus, on urns, tombs walls, masks, and as time goes by on various papyrus [papyri for snobs].
Spells 991: To become Sobek. I am the seed which issued from the encircling wrapping. I am he who broke the teeth of him who cut away the iron. I am the Lord of strength and might who took crocodile-shape. I am the Lord of wrong who lives on woe. I am that crocodile whose tongue was cut out because of the mutilation of Osiris. I am he who puts fear whom the Ennead fear. I am that god who rises in the East and sets in the West, to whom the Niles are given. I am that god whom the eight row. I am Sobek, the rebel who is among you[the gods]; you cannot do anything against me, you spirits or you dead, for I have taken possession of the sky and have taken possession of the earth.
During the Middle Kingdom Sobek will become a fairly important god (that is when Krokodilopolis is founded after all), specifically during Amenhamat 3, and by the way, the first attested female Pharaoh is Sobekneferu (see the Sobek). This spell is quite interesting (to say the least). just see that Sobek is clearly referred to not being a member of the Ennead. Not only that but "the 8 row for him", they 8 are the Ogdoad. So we clearly are confronted to a pretty powerful god, depicted as a rebel among the god and fairly over both the "oads". So we can put Sobek in the place of Ouranous. Old god of immense power and technically a primordial god.
Another interesting spell is the 158 where Sobek is plunging in the Nile to retrieve Horus's severed hand:
Ra said: "This son of Isis is injured by reason of what his mother herself has done to him; would that we might fetch Sobek from the back of the waters, that he may fish them out and so that his mother Isis may cause them to grow (again) in their proper place". And Sobek from the back of the waters said: "I have fished and I have sought; they slipped from my hand upon the banks of the waters, but I fished them up in the end with a fish-trap", that is how the fish-trap came into being.
This is where you see originated Sobek-Horus a pretty important deity during Middle Kingdom.
the final time of Egypt (Ramses was from this time, and no pyramids, no Hollywood), the new Kingdom is where Egypt will be at his apogee, most known Pharoah (Seti, Ram(es)ses, Hatchepsut) are from that time. One founding book is the conflict [contending] between Horus and Seth. In the passage I will cite, Re is writing a letter [Toth is the one writing Re cannot write] to Neith.
To wit: your humble servant, spend all night on Osiris's behalf consulting the Two Lands every day, while Sobek endures forever.
Let's translate this passage: Ra, the sun, is vanishing every day, so he cannot see what is happening constantly, contrary to both Neith, the sky, and Sobek his son, the Nile. Hence he is asking Neith advice. Which shows also the quite complex relationship between Egyptian gods.
During the New Kingdom, a new entity Sobek-Ra (clearly inspired by Sobek-Horus) will come. Most illustration you find with Sobek and the headdress as a sun is from the late New Kingdom.
Set and Sobek
Some authors mention that Sobek is the son of Set, just because of the close relationship between Set and the crocodiles [msh in old Egyptian, written with an owl (m), a lock (s), a rope (h), then a crocodile]. Notice that Sobek both in Middle and old Kingdom is fairly highly revered and one as to see that Sobek represent the strength of the crocodile when Set is destructive nature. it is also evident that during the Old kingdom Sobek was less reliable, without being linked with Set.
Sobek is an incredibly old deity worshipped until the very last end of Egypt (around 300 CE). It becomes central during Middle Kingdom in LOTS of stories (I skipped a lot of them to keep things simple). He is traditionally associated with Horus, Amon or Ra. He is not a part of the "oads" but generally over them.
Hierogl An handy hieroglyphic dictionary. Unfortunately in French.