FAIRMol

Z275021378

Pose ID 5962 Compound 764 Pose 544

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
T09
L. major DHFR-TS L. major
Ligand Z275021378

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 mixed SASA done
Strain ΔE
10.0 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.00
Burial
83%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 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. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.857 kcal/mol/HA) ✓ Good fit quality (FQ -8.27) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (10.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-25.707
kcal/mol
LE
-0.857
kcal/mol/HA
Fit Quality
-8.27
FQ (Leeson)
HAC
30
heavy atoms
MW
426
Da
LogP
3.53
cLogP
Final rank
2.6128
rank score
Inter norm
-0.851
normalised
Contacts
15
H-bonds 3
Strain ΔE
10.0 kcal/mol
SASA buried
83%
Lipo contact
81% BSA apolar/total
SASA unbound
684 Ų
Apolar buried
458 Ų

Interaction summary

HBA 1 HY 11 PI 3 CLASH 5

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.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap11Native recall0.52
Jaccard0.44RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU: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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
563 1.2449465497599101 -0.855232 -24.4706 3 17 0 0.00 0.00 - no Open
544 2.6127838836434134 -0.850618 -25.7067 3 15 11 0.52 0.00 - no Current
537 3.5425779970409126 -0.902631 -22.7767 6 18 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 -25.707kcal/mol
Ligand efficiency (LE) -0.8569kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.266
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 426.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.53
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 24.76kcal/mol
Minimised FF energy 14.75kcal/mol

SASA & burial

✓ computed
SASA (unbound) 684.2Ų
Total solvent-accessible surface area of free ligand
BSA total 565.7Ų
Buried surface area upon binding
BSA apolar 457.8Ų
Hydrophobic contacts buried
BSA polar 107.9Ų
Polar contacts buried
Fraction buried 82.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3329.0Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1661.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)