Protein family
Protein sequence
Protein function
Catalytic activity
EC number
EC number description
1.1.1.37
Oxidoreductases;
Acting on the CH-OH group of donors;
With NAD+ or NADP+ as acceptor;
malate dehydrogenase
1.1.1.399
Oxidoreductases;
Acting on the CH-OH group of donors;
With NAD+ or NADP+ as acceptor;
2-oxoglutarate reductase
1.1.1.95
Oxidoreductases;
Acting on the CH-OH group of donors;
With NAD+ or NADP+ as acceptor;
phosphoglycerate dehydrogenase
| PDB | Resolution (Å) | PDB name |
|---|---|---|
| 2G76 | 1.7 | Crystal structure of human 3-phosphoglycerate dehydrogenase |
| 5N53 | 1.48 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide |
| 5N6C | 2.3 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with NAD and L-Tartrate |
| 5NZO | 1.29 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 1-methyl-3-phenyl-1H-pyrazol-5-amine |
| 5NZP | 1.3 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-Hydroxybenzisoxazole |
| 5NZQ | 1.5 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-(1,3-oxazol-5-yl)aniline. |
| 5OFM | 1.5 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-amino-1-methyl-1H-indole |
| 5OFV | 1.5 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 5-fluoro-2-methylbenzoic acid |
| 5OFW | 1.5 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-Chloro-4-fluorobenzamide |
| 6CWA | 1.77 | CRYSTAL STRUCTURE PHGDH IN COMPLEX WITH NADH AND 3-PHOSPHOGLYCERATE AT 1.77 A RESOLUTION |
| 6PLF | 1.7 | Crystal structure of human PHGDH complexed with Compound 1 |
| 6PLG | 2.93 | Crystal structure of human PHGDH complexed with Compound 15 |
| 6RIH | 2.15 | Crystal structure of PHGDH in complex with compound 9 |
| 6RJ2 | 2.0 | Crystal structure of PHGDH in complex with compound 40 |
| 6RJ3 | 1.42 | Crystal structure of PHGDH in complex with compound 15 |
| 6RJ5 | 1.89 | Crystal structure of PHGDH in complex with compound 39 |
| 6RJ6 | 1.984 | Crystal structure of PHGDH in complex with BI-4924 |
| 7CVP | 2.5 | The Crystal Structure of human PHGDH from Biortus. |
| 7DKM | 1.7 | PHGDH covalently linked to oridonin |
| 7EWH | 2.99 | Crystal structure of human PHGDH in complex with Homoharringtonine |
| 7VA1 | 1.74 | Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with GDD-04-35 |
| GO ontology
|
GO term | GO description |
|---|---|---|
| Biological Process | GO:0070314 | G1 to G0 transition |
| Biological Process | GO:0006564 | L-serine biosynthetic process |
| Biological Process | GO:0007420 | brain development |
| Biological Process | GO:0009448 | gamma-aminobutyric acid metabolic process |
| Biological Process | GO:0021782 | glial cell development |
| Biological Process | GO:0006541 | glutamine metabolic process |
| Biological Process | GO:0006544 | glycine metabolic process |
| Biological Process | GO:0021915 | neural tube development |
| Biological Process | GO:0031175 | neuron projection development |
| Biological Process | GO:0010468 | regulation of gene expression |
| Biological Process | GO:0021510 | spinal cord development |
| Biological Process | GO:0019530 | taurine metabolic process |
| Biological Process | GO:0006566 | threonine metabolic process |
| Molecular Function | GO:0030060 | L-malate dehydrogenase activity |
| Molecular Function | GO:0051287 | NAD binding |
| Molecular Function | GO:0009055 | electron transfer activity |
| Molecular Function | GO:0004617 | phosphoglycerate dehydrogenase activity |
| Cellular Component | GO:0005829 | cytosol |
| Cellular Component | GO:0070062 | extracellular exosome |
| InterPro
|
InterPro name |
|---|---|
| IPR006139 | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain |
| IPR006140 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain |
| IPR006236 | D-3-phosphoglycerate dehydrogenase |
| IPR029009 | Allosteric substrate binding domain superfamily |
| IPR029752 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 |
| IPR029753 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site |
| IPR036291 | NAD(P)-binding domain superfamily |
| IPR045626 | D-3-phosphoglycerate dehydrogenase, ASB domain |
| Pfam
|
Pfam name |
|---|---|
| PF00389 | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain |
| PF02826 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain |
| PF19304 | D-3-phosphoglycerate dehydrogenase intervening domain |
| Reactome
|
Reactome Name | Node type
|
Reactome Root | Reactome Root Name |
|---|---|---|---|---|
| R-HSA-977347 | Serine biosynthesis | Leaf | R-HSA-1430728 | Metabolism |
| HPO ID
|
HPO name |
|---|---|
| HP:0000007 | Autosomal recessive inheritance |
| HP:0000023 | Inguinal hernia |
| HP:0000028 | Cryptorchidism |
| HP:0000104 | Renal agenesis |
| HP:0000135 | Hypogonadism |
| HP:0000136 | Bifid uterus |
| HP:0000175 | Cleft palate |
| HP:0000179 | Thick lower lip vermilion |
| HP:0000204 | Cleft upper lip |
| HP:0000252 | Microcephaly |
| HP:0000316 | Hypertelorism |
| HP:0000340 | Sloping forehead |
| HP:0000347 | Micrognathia |
| HP:0000369 | Low-set ears |
| HP:0000400 | Macrotia |
| HP:0000445 | Wide nose |
| HP:0000457 | Depressed nasal ridge |
| HP:0000470 | Short neck |
| HP:0000475 | Broad neck |
| HP:0000518 | Cataract |
| HP:0000519 | Developmental cataract |
| HP:0000520 | Proptosis |
| HP:0000561 | Absent eyelashes |
| HP:0000565 | Esotropia |
| HP:0000568 | Microphthalmia |
| HP:0000639 | Nystagmus |
| HP:0000708 | Atypical behavior |
| HP:0000737 | Irritability |
| HP:0001059 | Pterygium |
| HP:0001181 | Adducted thumb |
| HP:0001196 | Short umbilical cord |
| HP:0001249 | Intellectual disability |
| HP:0001250 | Seizure |
| HP:0001257 | Spasticity |
| HP:0001274 | Agenesis of corpus callosum |
| HP:0001276 | Hypertonia |
| HP:0001305 | Dandy-Walker malformation |
| HP:0001321 | Cerebellar hypoplasia |
| HP:0001339 | Lissencephaly |
| HP:0001508 | Failure to thrive |
| HP:0001510 | Growth delay |
| HP:0001511 | Intrauterine growth retardation |
| HP:0001537 | Umbilical hernia |
| HP:0001558 | Decreased fetal movement |
| HP:0001561 | Polyhydramnios |
| HP:0001629 | Ventricular septal defect |
| HP:0001643 | Patent ductus arteriosus |
| HP:0001655 | Patent foramen ovale |
| HP:0001669 | Transposition of the great arteries |
| HP:0001770 | Toe syndactyly |
| HP:0001838 | Rocker bottom foot |
| HP:0001848 | Calcaneovalgus deformity |
| HP:0001873 | Thrombocytopenia |
| HP:0001889 | Megaloblastic anemia |
| HP:0001989 | Fetal akinesia sequence |
| HP:0001999 | Abnormal facial shape |
| HP:0002013 | Vomiting |
| HP:0002020 | Gastroesophageal reflux |
| HP:0002069 | Bilateral tonic-clonic seizure |
| HP:0002079 | Hypoplasia of the corpus callosum |
| HP:0002089 | Pulmonary hypoplasia |
| HP:0002119 | Ventriculomegaly |
| HP:0002121 | Generalized non-motor (absence) seizure |
| HP:0002123 | Generalized myoclonic seizure |
| HP:0002190 | Choroid plexus cyst |
| HP:0002305 | Athetosis |
| HP:0002324 | Hydranencephaly |
| HP:0002414 | Spina bifida |
| HP:0002510 | Spastic tetraplegia |
| HP:0002521 | Hypsarrhythmia |
| HP:0002536 | Abnormal cortical gyration |
| HP:0002983 | Micromelia |
| HP:0003577 | Congenital onset |
| HP:0003811 | Neonatal death |
| HP:0003826 | Stillbirth |
| HP:0004322 | Short stature |
| HP:0006101 | Finger syndactyly |
| HP:0006266 | Small placenta |
| HP:0006808 | Cerebral hypomyelination |
| HP:0006872 | Cerebral hypoplasia |
| HP:0007266 | Cerebral dysmyelination |
| HP:0007281 | Developmental stagnation |
| HP:0007430 | Generalized edema |
| HP:0007503 | Generalized ichthyosis |
| HP:0007525 | Yellow subcutaneous tissue covered by thin, scaly skin |
| HP:0008064 | Ichthyosis |
| HP:0008734 | Decreased testicular size |
| HP:0009466 | Radial deviation of finger |
| HP:0009473 | Joint contracture of the hand |
| HP:0009826 | Limb undergrowth |
| HP:0010719 | Abnormality of hair texture |
| HP:0010819 | Atonic seizure |
| HP:0010821 | Focal emotional seizure with laughing |
| HP:0011097 | Epileptic spasm |
| HP:0011224 | Ablepharon |
| HP:0011343 | Moderate global developmental delay |
| HP:0011344 | Severe global developmental delay |
| HP:0011451 | Primary microcephaly |
| HP:0011968 | Feeding difficulties |
| HP:0012277 | Hypoglycinemia |
| HP:0012279 | Hyposerinemia |
| HP:0012385 | Camptodactyly |
| HP:0012444 | Brain atrophy |
| HP:0012448 | Delayed myelination |
| HP:0012762 | Cerebral white matter atrophy |
| HP:0030084 | Clinodactyly |
| HP:0030215 | Inappropriate crying |
| HP:0031244 | Swollen lip |
| HP:0034691 | Reduced 3-phosphoglycerate dehydrogenase activity |
| HP:0100633 | Esophagitis |
| HP:0100704 | Cerebral visual impairment |
| HP:0100807 | Long fingers |
| Disease name | MONDO ID
|
ICD10
|
ICD10 chapter
|
OMIM
|
Orphanet
|
|---|---|---|---|---|---|
| neu-laxova syndrome 1 | MONDO:0009736 | Q87 | chapter17, Congenital malformations, deformations and chromosomal abnormalities | OMIM:256520 | Orphanet:583607 |
| phgdh deficiency | MONDO:0011152 | E72 | chapter4, Endocrine, nutritional and metabolic diseases | OMIM:601815 | Orphanet:79351 |