FAIRMol

TC488

Pose ID 1645 Compound 1436 Pose 290

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T03
L. major DHFR L. major
Ligand TC488

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
35.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.65, Jaccard 0.48, H-bond role recall 0.00
Burial
91%
Hydrophobic fit
87%
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.738 kcal/mol/HA) ✓ Good fit quality (FQ -7.61) ✓ Good H-bonds (4 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Very high strain energy (35.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (19)
Score
-28.031
kcal/mol
LE
-0.738
kcal/mol/HA
Fit Quality
-7.61
FQ (Leeson)
HAC
38
heavy atoms
MW
515
Da
LogP
5.18
cLogP
Final rank
4.0977
rank score
Inter norm
-0.785
normalised
Contacts
20
H-bonds 5
Strain ΔE
35.2 kcal/mol
SASA buried
91%
Lipo contact
87% BSA apolar/total
SASA unbound
815 Ų
Apolar buried
646 Ų

Interaction summary

HBD 2 HBA 2 HY 9 PI 1 CLASH 2

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.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap13Native recall0.65
Jaccard0.48RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; 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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
290 4.097676844008653 -0.78523 -28.0312 5 20 13 0.65 0.00 - no Current
215 4.595874156107308 -0.890462 -29.8082 11 22 0 0.00 0.00 - no Open
176 5.855540308270551 -0.790924 -25.3763 12 21 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -28.031kcal/mol
Ligand efficiency (LE) -0.7377kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.605
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 514.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.18
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 144.30kcal/mol
Minimised FF energy 109.11kcal/mol

SASA & burial

✓ computed
SASA (unbound) 814.8Ų
Total solvent-accessible surface area of free ligand
BSA total 741.0Ų
Buried surface area upon binding
BSA apolar 645.9Ų
Hydrophobic contacts buried
BSA polar 95.1Ų
Polar contacts buried
Fraction buried 91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1744.2Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 791.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)