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Models
The homology models of GPCRs were produced using the beta2-adrenergic receptor and rhodopsin crystal structures in the inactive (2rh1.pdb, 1u19.pdb) and active (3sn6.pdb, 3dqb.pdb) conformations as templates and refined using distance geometry calculations with DIANA. Inactive conformations of opioid receptor were generated using corresponding crystal structures of mu- (4dkl.pdb), delta- (4ej4.pdb), kappa- (4djh.pdb) opioid receptors and nociceptin/orphanin FQ receptor (4ea3.pdb). Active conformation of the mu-opioid receptor with natural agonist endomorphin-1 was generated by DIANA using constraints from the inactive mu-opioid receptor (4dkl.pdb), active beta2-adrenergic receptor (3sn6.pdb) and specific ligand-receptor hydrogen bonds. Active conformations for other opioid receptors were generated using the model of the active mu-opioid receptor as a structural template. The ligand conformations were derived from their crystal structures or previously developed pharmacophore models. The ligand docking was guided by experimentally-derived receptor-ligand interactions and assisted by the Solid Docking module of QUANTA (Accelrys, Inc.) Abbreviations: I – inactive conformation, A –active conformation, D – refined model by DIANA calculation.

Model Title Model Description Download Text
GnRHR_HUMAN_AD_GnRH Human gonadotropin-releasing hormone receptor (active state, residues 11-328) with GnRH (residues 1-10) and C-terminus of Gq (residues 330-359) Download Text
GnRHR_HUMAN_ID_cetrorelix Human gonadotropin-releasing hormone receptor (inactive state, residues 11-328) with cetrorelix (residues 1-10) Download Text
MC1R_HUMAN_ID_ASIP MC1 melanocortin receptor (inactive state, residues 35-317) with ASIP (residues 93-132) Download Text
MC2R_HUMAN_AD_ACTH ACTH receptor (active state, residues 12-295) with ACTH (residues 1-24) Download Text
MC4R_HUMAN_AD_AMSH MC4 melanocortin receptor (active state, residues 28-321) with alpha-MSH, Ac-Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro-Val-NH2 Download Text
MC4R_HUMAN_AD_MB243 MC4 melanocortin receptor (active state, residues 28-321) with MB243 (agonist) Download Text
MC4R_HUMAN_AD_NDPMSH MC4 melanocortin receptor (active state, residues 28-321) with NDP-MSH, Ac-Ser-Tyr-Ser-Nle-Glu-His-DPhe-Arg-Trp-Gly-Lys-Pro-Val-NH2 Download Text
MC4R_HUMAN_AD_THIQ MC4 melanocortin receptor (active state, residues 28-321) with THIQ (agonist) Download Text
MC4R_HUMAN_ID_AGRP MC4 melanocortin receptor (inactive state, residues 40-321) with AGRP (residues 87-132) Download Text
MC4R_HUMAN_ID_ASIP MC4 melanocortin receptor (inactive state, residues 40-321) with ASIP (residues 93-132) Download Text
OPRD_HUMAN_A_JOM13 Human delta opioid receptor (active state, residues 45-334) with JOM13, Tyr-c(SS)[DCys-Phe-DPen]OH Download Text
OPRD_HUMAN_A_MP143 Human delta opioid receptor (active state, residues 45-334) with MP143, Tyr-c(SS)[DCys-Phe-Phe-Cys]NH2 Download Text
OPRD_HUMAN_A_MP151 Human delta opioid receptor (active state, residues 45-334) with MP151, Tyr-c(SMeS)[DCys-Phe-Phe-Cys]NH2 Download Text
OPRD_HUMAN_I_LP13M Human delta opioid receptor (inactive state, residues 41-333) with LP13M, Tyr-c(SMeS)[DCys-Phe-2Nal-Cys]NH2 Download Text
OPRD_MOUSE_I_KSK103 Mouse delta opioid receptor (inactive state, residues 41-333) with KSK103, Dmt-c(SEtS)[DCys-Aci-DPen]OH Download Text
OPRD_MOUSE_I_MP151 Mouse delta opioid receptor (inactive state, residues 41-333) with MP151, Tyr-c(SMeS)[DCys-Phe-Phe-Cys]NH2 Download Text
OPRK_HUMAN_A_MP143 Human kappa opioid receptor (active state, residues 55-346) with MP143, Tyr-c(SS)[DCys-Phe-Phe-Cys]NH2 Download Text
OPRK_HUMAN_A_MP148 Human kappa opioid receptor (active state, residues 55-346) with peptide 10 or MP148, Tyr-c(SS)[DCys-Phe-Phe-DCys]NH2 Download Text
OPRK_HUMAN_I_KSK102 Human kappa opioid receptor (inactive state, residues 55-347) with KSK102, Dmt-c(SEtS)[DCys-Aci-DPen]NH2 Download Text
OPRK_HUMAN_I_norBNI Human kappa opioid receptor (inactive state, residues 55-347) with norBNI (antagonist) Download Text
OPRM_MOUSE_AD_EM1 Mouse mu opioid receptor (active state, residues 64-352) with endomorphin-1 (agonist), Tyr-Pro-Trp-Phe-NH2 Download Text
OPRM_MOUSE_A_DmtDALDA Mouse mu opioid receptor (active state, residues 64-352) with Dmt-DALDA (agonist), Dmt-DArg-Phe-Lys-NH2 Download Text
OPRM_MOUSE_A_JOM6 Mouse mu opioid receptor (active state, residues 64-352) with JOM6, Tyr-c(SEtS)[DCys-Phe-DPen]NH2 Download Text
OPRM_MOUSE_A_KSK103 Mouse mu opioid receptor (active state, residues 64-352) with KSK103, Dmt-c(SEtS)[DCys-Aci-DPen]OH Download Text
OPRM_MOUSE_A_LP13M Mouse mu opioid receptor (active state, residues 64-352) with LP13M, Tyr-c(SMeS)[DCys-Phe-2Nal-Cys]NH2 Download Text
OPRM_MOUSE_A_morphiceptin Mouse mu opioid receptor (active state, residues 64-352) with morphiceptin, Tyr-Pro-Phe-Pro-NH2 Download Text
OPRM_MOUSE_A_morphine Mouse mu opioid receptor (active state, residues 64-352) with morphine Download Text
OPRM_MOUSE_A_MP143 Mouse mu opioid receptor (active state, residues 64-352) with MP143, Tyr-c(SS)[DCys-Phe-Phe-Cys]NH2 Download Text
OPRM_MOUSE_A_MP151 Mouse mu opioid receptor (active state, residues 64-352) with MP151, Tyr-c(SMeS)[DCys-Phe-Phe-Cys]NH2 Download Text
OPRM_MOUSE_ID_antanal2 Mouse mu opioid receptor (inactive state, residues 65-351) with antanal2 (antagonist), Dmt-Pro-Phe-D-2Nal-NH2 Download Text
OPRX_HUMAN_A_nociceptin Human nociceptin receptor, NOP (active state, residues 47-333), with nociceptin, Phe-Gly-Gly-Phe-Thr-Gly-Ala-Arg-Lys-Ser-Ala-Arg-Lys-Leu-Ala-Asn-Gln Download Text
OPRX_HUMAN_I_UFP101 Human nociceptin receptor, NOP (inactive state, residues 47-335), with UFP101 (antagonist), N(Bn)Gly-Gly-Gly-Phe-Thr-Gly-Ala-Arg-Lys-Ser-Ala-Arg-Lys-Arg-Lys-Asn-Gln-NH2 Download Text



Viewer links

PyMOL , A USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation




Database links

Protein Data Bank (PDB) , An archive of experimentally determined 3D-structures of biological macromolecule

SWISS-PROT and TrEMBL , protein knowledgebase

SCOP , Structural Classification of Proteins

CATH , Hierarchical classification of protein structural relationships

FSSP , Families of structurally similar proteins

PFAM , Database of multiple sequence alignments

GPCRDB , Database of G-protein coupled proteins

GPCRDBsup , Supplement to GPCRDB

ModBase , Database of 3D protein models

Membranome , Our database of all human membrane proteins

Orientations of Proteins in Membranes (OPM) database , Our database that displays the tilt angles, hydrophobic thicknesses, delta G transfer, and other characteristics of transmembrane and periperal membrane proteins




Server links

BLAST , Sequence alignment tools

3D-pssm , Fold recognition server

PSIPRED , A protein structure prediction server

PHDsec , PredictProtein server at EMBL

Prediction Center , Protein Structure Prediction Center

SWISS-MODEL , Protein structure homology-modeling server

TMpred , Prediction of Transmembrane Regions and Orientation




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