5HNB | pdb_00005hnb

CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone

PDB DOI: https://doi.org/10.2210/pdb5HNB/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-01-18 Released: 2016-04-27
Deposition Author(s): Musil, D., Blagg, J., Schiemann, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.252 (Depositor), 0.260 (DCC)
R-Value Work:
0.217 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone

Schiemann, K.

To be published.

Macromolecule Content

Total Structure Weight: 75.53 kDa
Atom Count: 5,261
Modeled Residue Count: 608
Deposited Residue Count: 636
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase 8	A	370	Homo sapiens	Mutation(s): 0 Gene Names: CDK8 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49336 (Homo sapiens) Explore P49336 Go to UniProtKB: P49336
PHAROS: P49336 GTEx: ENSG00000132964
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49336
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-C	B	266	Homo sapiens	Mutation(s): 0 Gene Names: CCNC
UniProt & NIH Common Fund Data Resources
Find proteins for P24863 (Homo sapiens) Explore P24863 Go to UniProtKB: P24863
PHAROS: P24863 GTEx: ENSG00000112237
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P24863
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
62M Query on 62M Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	[6-hydroxy-3-(3-methylbenzyl)-1H-indazol-5-yl][(3S)-3-hydroxypyrrolidin-1-yl]methanone C₂₀ H₂₁ N₃ O₃ MTAMTSBOGRBXGX-AWEZNQCLSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], K [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B]