Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T04

L. major PTR1 L. major

Ligand Z18498694

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 high Native mixed SASA done

Strain ΔE

16.8 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20

Burial

85%

Hydrophobic fit

72%

Reason: no major geometry red flags detected

2 protein-contact clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.454 kcal/mol/HA) ✓ Good fit quality (FQ -11.37) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Moderate strain (16.8 kcal/mol) ✗ Geometry warnings

Score

-24.721

kcal/mol

-1.454

kcal/mol/HA

Fit Quality

-11.37

FQ (Leeson)

HAC

heavy atoms

253

LogP

0.87

cLogP

Final rank

0.8643

rank score

Inter norm

-1.476

normalised

Contacts

H-bonds 2

Strain ΔE

16.8 kcal/mol

SASA buried

85%

Lipo contact

72% BSA apolar/total

SASA unbound

472 Å²

Apolar buried

291 Å²

Interaction summary

HBA 2 HY 5 PI 4 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	7PXX	Contacts	19
Pose	Open native pose	HB	0
IFP residues	ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap	10	Native recall	0.53
Jaccard	0.53	RMSD	-
HB strict	1	Strict recall	0.17
HB same residue+role	1	HB role recall	0.20
HB same residue	1	HB residue recall	0.20

Protein summary

308 residues

Protein target	T04	Atoms	4210
Residues	308	Chains	3
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
455	0.8643064675439239	-1.4763	-24.7212	2	10	10	0.53	0.20	-	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 -24.721kcal/mol

Ligand efficiency (LE) -1.4542kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.371

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

Heavy atom count 17HA

Physicochemical properties

Molecular weight 253.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.87

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 16.76kcal/mol

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

Docked FF energy -62.50kcal/mol

Minimised FF energy -79.26kcal/mol

SASA & burial

✓ computed

SASA (unbound) 471.9Å²

Total solvent-accessible surface area of free ligand

BSA total 402.3Å²

Buried surface area upon binding

BSA apolar 290.6Å²

Hydrophobic contacts buried

BSA polar 111.8Å²

Polar contacts buried

Fraction buried 85.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 72.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1510.5Å²

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 1028.5Å²

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