Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T07

T. brucei PTR1 T. brucei

Ligand ulfkktlib_3178

PDB6RX6↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Promising SASA cached

Promising and worth follow-up

Binding strong Geometry high Native strong SASA done

Strain ΔE

15.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.53, Jaccard 0.48, H-bond role recall 0.80

Burial

95%

Hydrophobic fit

60%

Reason: no major geometry red flags detected

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.846

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.647

ADMET + ECO + DL

ADMETscore (GDS)

0.669

absorption · distr. · metab.

DLscore

0.488

drug-likeness

P(SAFE)

0.21

GDS classification

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.985 kcal/mol/HA) ✓ Good fit quality (FQ -15.52) ✓ Deep burial (95% SASA buried) ✗ Moderate strain (15.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-33.740

kcal/mol

-1.985

kcal/mol/HA

Fit Quality

-15.52

FQ (Leeson)

HAC

heavy atoms

229

LogP

0.21

cLogP

Final rank

0.3785

rank score

Inter norm

-1.801

normalised

Contacts

H-bonds 6

Strain ΔE

15.6 kcal/mol

SASA buried

95%

Lipo contact

60% BSA apolar/total

SASA unbound

392 Å²

Apolar buried

221 Å²

Interaction summary

HBD 1 HY 5 PI 2 CLASH 2

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	TbPTR1_cW_6RX6_Ready	Contacts	19
Pose	Open native pose	HB	0
IFP residues	ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap	10	Native recall	0.53
Jaccard	0.48	RMSD	-
HB strict	3	Strict recall	0.50
HB same residue+role	4	HB role recall	0.80
HB same residue	4	HB residue recall	0.80

Protein summary

275 residues

Protein target	T07	Atoms	3932
Residues	275	Chains	3
Residue summary	LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
210	0.37848073417416145	-1.80073	-33.7398	6	12	10	0.53	0.80	-	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 -33.740kcal/mol

Ligand efficiency (LE) -1.9847kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -15.520

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

Heavy atom count 17HA

Physicochemical properties

Molecular weight 229.2Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.21

Lipinski: ≤ 5

Rotatable bonds 1

Conformational strain (MMFF94s)

Strain energy (ΔE) 15.55kcal/mol

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

Docked FF energy 81.79kcal/mol

Minimised FF energy 66.24kcal/mol

SASA & burial

✓ computed

SASA (unbound) 391.9Å²

Total solvent-accessible surface area of free ligand

BSA total 371.2Å²

Buried surface area upon binding

BSA apolar 220.8Å²

Hydrophobic contacts buried

BSA polar 150.4Å²

Polar contacts buried

Fraction buried 94.7%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 59.5%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1356.7Å²

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 2051.9Å²

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

Complex non-polar SASA 931.0Å²

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