Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T09

L. major DHFR-TS L. major

Ligand Z16042263

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 high Native strong SASA done

Strain ΔE

28.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00

Burial

88%

Hydrophobic fit

87%

Reason: no major geometry red flags detected

1 protein-contact clashes 36% of hydrophobic surface appears solvent-exposed (9/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.698 kcal/mol/HA) ✓ Good fit quality (FQ -6.80) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ High strain energy (28.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)

Score

-21.645

kcal/mol

-0.698

kcal/mol/HA

Fit Quality

-6.80

FQ (Leeson)

HAC

heavy atoms

429

LogP

4.60

cLogP

Final rank

3.0041

rank score

Inter norm

-0.837

normalised

Contacts

H-bonds 2

Strain ΔE

28.7 kcal/mol

SASA buried

88%

Lipo contact

87% BSA apolar/total

SASA unbound

710 Å²

Apolar buried

543 Å²

Interaction summary

HBD 1 HBA 1 HY 8 PI 3 CLASH 1

HBD/HBA · H-bonds (geometric)

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

Name	3CL9	Contacts	21
Pose	Open native pose	HB	0
IFP residues	NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap	13	Native recall	0.62
Jaccard	0.50	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	0	HB role recall	0.00
HB same residue	0	HB residue recall	0.00

Protein summary

511 residues

Protein target	T09	Atoms	8170
Residues	511	Chains	2
Residue summary	LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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
649	3.004115133606733	-0.837059	-21.6449	2	18	13	0.62	0.00	-	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 -21.645kcal/mol

Ligand efficiency (LE) -0.6982kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.802

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

Heavy atom count 31HA

Physicochemical properties

Molecular weight 428.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.60

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 28.69kcal/mol

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

Docked FF energy 57.38kcal/mol

Minimised FF energy 28.69kcal/mol

SASA & burial

✓ computed

SASA (unbound) 709.6Å²

Total solvent-accessible surface area of free ligand

BSA total 625.0Å²

Buried surface area upon binding

BSA apolar 543.1Å²

Hydrophobic contacts buried

BSA polar 81.9Å²

Polar contacts buried

Fraction buried 88.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 86.9%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3375.1Å²

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 4428.5Å²

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

Complex non-polar SASA 1670.0Å²

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