Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T06

T. brucei DHFR T. brucei

Ligand Z56799025

PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Likely artefact or unreliable pose

Binding weak Geometry low Native strong SASA done

Strain ΔE

72.1 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.81, Jaccard 0.68, H-bond role recall 1.00

Burial

94%

Hydrophobic fit

64%

Reason: strain 72.1 kcal/mol

strain ΔE 72.1 kcal/mol 4 protein-contact clashes 4 intramolecular clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Extreme strain energy (72.1 kcal/mol) ✗ Low LE (-0.134 kcal/mol/HA) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Internal clashes (6)

Score

-4.154

kcal/mol

-0.134

kcal/mol/HA

Fit Quality

-1.30

FQ (Leeson)

HAC

heavy atoms

449

LogP

5.48

cLogP

Final rank

1.1401

rank score

Inter norm

-0.845

normalised

Contacts

H-bonds 6

Strain ΔE

72.1 kcal/mol

SASA buried

94%

Lipo contact

64% BSA apolar/total

SASA unbound

723 Å²

Apolar buried

437 Å²

Interaction summary

HBD 1 HY 10 PI 4 CLASH 4

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	8RHT	Contacts	21
Pose	Open native pose	HB	0
IFP residues	ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap	17	Native recall	0.81
Jaccard	0.68	RMSD	-
HB strict	4	Strict recall	0.80
HB same residue+role	4	HB role recall	1.00
HB same residue	4	HB residue recall	1.00

Protein summary

223 residues

Protein target	T06	Atoms	3452
Residues	223	Chains	1
Residue summary	ARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:NDP301

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
375	1.1401165276232816	-0.845437	-4.15408	6	21	17	0.81	1.00	-	no	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -4.154kcal/mol

Ligand efficiency (LE) -0.1340kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -1.305

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 31HA

Physicochemical properties

Molecular weight 449.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 5.48

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 72.08kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy 48.42kcal/mol

Minimised FF energy -23.66kcal/mol

SASA & burial

✓ computed

SASA (unbound) 723.1Å²

Total solvent-accessible surface area of free ligand

BSA total 683.3Å²

Buried surface area upon binding

BSA apolar 437.1Å²

Hydrophobic contacts buried

BSA polar 246.2Å²

Polar contacts buried

Fraction buried 94.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 64.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1689.3Å²

SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.

Receptor non-polar SASA 1808.8Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 591.2Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)