Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T05

L. major PTR1 L. major

Ligand OHD_TB2020_58

PDB7PXX↗

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 medium Native strong SASA done

Strain ΔE

11.9 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.59, Jaccard 0.53, H-bond role recall 0.50

Burial

90%

Hydrophobic fit

80%

Reason: no major geometry red flags detected

1 protein-contact clashes 3 intramolecular clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.268 kcal/mol/HA) ✓ Good fit quality (FQ -11.01) ✓ Good H-bonds (3 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Moderate strain (11.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (7)

Score

-27.900

kcal/mol

-1.268

kcal/mol/HA

Fit Quality

-11.01

FQ (Leeson)

HAC

heavy atoms

309

LogP

2.47

cLogP

Final rank

0.2963

rank score

Inter norm

-1.327

normalised

Contacts

H-bonds 5

Strain ΔE

11.9 kcal/mol

SASA buried

90%

Lipo contact

80% BSA apolar/total

SASA unbound

496 Å²

Apolar buried

360 Å²

Interaction summary

HBD 1 HBA 2 HY 4 PI 4 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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	ligand	Contacts	17
Pose	Open native pose	HB	0
IFP residues	ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap	10	Native recall	0.59
Jaccard	0.53	RMSD	-
HB strict	3	Strict recall	0.43
HB same residue+role	3	HB role recall	0.50
HB same residue	3	HB residue recall	0.60

Protein summary

274 residues

Protein target	T05	Atoms	4108
Residues	274	Chains	2
Residue summary	LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
40	0.2962980136476223	-1.3267	-27.8997	5	12	10	0.59	0.50	-	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 -27.900kcal/mol

Ligand efficiency (LE) -1.2682kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.010

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

Heavy atom count 22HA

Physicochemical properties

Molecular weight 309.2Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.47

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 11.88kcal/mol

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

Docked FF energy -39.72kcal/mol

Minimised FF energy -51.60kcal/mol

SASA & burial

✓ computed

SASA (unbound) 496.4Å²

Total solvent-accessible surface area of free ligand

BSA total 447.5Å²

Buried surface area upon binding

BSA apolar 359.6Å²

Hydrophobic contacts buried

BSA polar 87.9Å²

Polar contacts buried

Fraction buried 90.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 80.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1524.7Å²

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 2179.4Å²

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

Complex non-polar SASA 1061.5Å²

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