Structure of PDB 9ci9 Chain A Binding Site BS03

Receptor Information

>9ci9 Chain A (length=424) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVS
YEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVME
IMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLP
QGVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERET
GFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSL
GGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHD
PVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRND
NDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNT
SGIQTEWSPPLTMLFLCATKFSAS

Ligand information

Ligand ID

0KX

InChI

InChI=1S/C9H17N4O12P3/c10-7-1-2-13(9(15)11-7)8-3-5(14)6(24-8)4-23-26(16,17)12-27(18,19)25-28(20,21)22/h1-2,5-6,8,14H,3-4H2,(H2,10,11,15)(H2,20,21,22)(H3,12,16,17,18,19)/t5-,6+,8+/m0/s1

InChIKey

STYMTWKSQLVXJN-SHYZEUOFSA-N

SMILES

Software	SMILES
CACTVS 3.370	NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2
CACTVS 3.370	NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2
OpenEye OEToolkits 1.7.6	C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O
OpenEye OEToolkits 1.7.6	C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O

Formula

C9 H17 N4 O12 P3

Name

2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine

PDB chain

9ci9 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	9ci9 DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta.
Resolution	2.09 Å
Binding residue (original residue number in PDB)	D13 M14 D15 C16 F17 F18 I48 Y52 R55 R61 D115 K231
Binding residue (residue number reindexed from 1)	D12 M13 D14 C15 F16 F17 I47 Y51 R54 R60 D114 K223
Annotation score	1

External links

PDB	RCSB:9ci9, PDBe:9ci9, PDBj:9ci9
PDBsum	9ci9
PubMed	39259676
UniProt	Q9Y253\|POLH_HUMAN DNA polymerase eta (Gene Name=POLH)

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