Structure of PDB 9chw Chain A Binding Site BS03

Receptor Information

>9chw Chain A (length=431) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGI
IAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASV
EVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYI
EGLPQGPTTVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMR
AAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMP
IRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAM
CRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEER
LTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFT
VIKNCNTSGIQTEWSPPLTMLFLCATKFSAS

Ligand information

Ligand ID

DZ4

InChI

InChI=1S/C10H17N6O11P3/c11-9-8-10(13-3-12-9)16(4-14-8)7-1-5(17)6(26-7)2-25-28(18,19)15-29(20,21)27-30(22,23)24/h3-7,17H,1-2H2,(H2,11,12,13)(H2,22,23,24)(H3,15,18,19,20,21)/t5-,6+,7+/m0/s1

InChIKey

WKIPJDSLGCBQCU-RRKCRQDMSA-N

SMILES

Software	SMILES
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)CC3O
CACTVS 3.370	Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0	c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.370	Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.7.0	c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H17 N6 O11 P3

Name

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

PDB chain

9chw 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	9chw DNA Replication across alpha-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase eta.
Resolution	2.16 Å
Binding residue (original residue number in PDB)	D13 M14 D15 C16 F17 F18 Y52 R55 R61 D115 K231
Binding residue (residue number reindexed from 1)	D16 M17 D18 C19 F20 F21 Y55 R58 R64 D118 K230
Annotation score	1

External links

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

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