Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T06

T. brucei DHFR T. brucei

Ligand TC428

PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry medium Native strong SASA done

Strain ΔE

32.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.71, Jaccard 0.65, H-bond role recall 0.25

Burial

97%

Hydrophobic fit

76%

Reason: no major geometry red flags detected

3 protein-contact clashes 3 intramolecular clashes

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.768

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.569

ADMET + ECO + DL

ADMETscore (GDS)

0.579

absorption · distr. · metab.

DLscore

0.434

drug-likeness

P(SAFE)

0.15

GDS classification

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-0.617 kcal/mol/HA) ✓ Good fit quality (FQ -5.68) ✓ Deep burial (97% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (32.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)

Score

-16.029

kcal/mol

-0.617

kcal/mol/HA

Fit Quality

-5.68

FQ (Leeson)

HAC

heavy atoms

352

LogP

1.56

cLogP

Final rank

1.9093

rank score

Inter norm

-0.992

normalised

Contacts

H-bonds 3

Strain ΔE

32.2 kcal/mol

SASA buried

97%

Lipo contact

76% BSA apolar/total

SASA unbound

623 Å²

Apolar buried

457 Å²

Interaction summary

HBD 1 HBA 1 HY 10 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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	15	Native recall	0.71
Jaccard	0.65	RMSD	-
HB strict	1	Strict recall	0.20
HB same residue+role	1	HB role recall	0.25
HB same residue	1	HB residue recall	0.25

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
235	1.909251575340555	-0.992154	-16.029	3	17	15	0.71	0.25	-	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 -16.029kcal/mol

Ligand efficiency (LE) -0.6165kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.680

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 352.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.56

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 32.17kcal/mol

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

Docked FF energy 64.50kcal/mol

Minimised FF energy 32.32kcal/mol

SASA & burial

✓ computed

SASA (unbound) 622.9Å²

Total solvent-accessible surface area of free ligand

BSA total 601.6Å²

Buried surface area upon binding

BSA apolar 457.3Å²

Hydrophobic contacts buried

BSA polar 144.3Å²

Polar contacts buried

Fraction buried 96.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 76.0%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1704.8Å²

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 574.6Å²

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