FAIRMol

Z29884022

Pose ID 2461 Compound 1766 Pose 428

DB SELECTIONDocking 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
T04
L. major PTR1 L. major
Ligand Z29884022
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 strong SASA done
Strain ΔE
13.4 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.40
Burial
81%
Hydrophobic fit
87%
Reason: no major geometry red flags detected
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.045 kcal/mol/HA) ✓ Good fit quality (FQ -9.50) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Moderate strain (13.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-26.124
kcal/mol
LE
-1.045
kcal/mol/HA
Fit Quality
-9.50
FQ (Leeson)
HAC
25
heavy atoms
MW
337
Da
LogP
3.24
cLogP
Strain ΔE
13.4 kcal/mol
SASA buried
81%
Lipo contact
87% BSA apolar/total
SASA unbound
603 Ų
Apolar buried
424 Ų

Interaction summary

HB 2 HY 18 PI 3 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank1.155Score-26.124
Inter norm-1.183Intra norm0.138
Top1000noExcludedno
Contacts11H-bonds2
Artifact reasongeometry warning; 9 clashes; 1 protein clash; 1 cofactor-context clash
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 TYR191 TYR194 VAL230 ARG287

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.58
Jaccard0.58RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
Residue summaryLEU: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

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
415 0.6019940514467164 -0.909601 -20.1474 0 17 0 0.00 0.00 - no Open
428 1.154995800561394 -1.18339 -26.1237 2 11 11 0.58 0.40 - no Current
457 3.1110710607896723 -0.826808 -17.3463 5 11 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 -26.124kcal/mol
Ligand efficiency (LE) -1.0449kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.500
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.24
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 72.67kcal/mol
Minimised FF energy 59.31kcal/mol

SASA & burial

✓ computed
SASA (unbound) 602.9Ų
Total solvent-accessible surface area of free ligand
BSA total 488.3Ų
Buried surface area upon binding
BSA apolar 424.1Ų
Hydrophobic contacts buried
BSA polar 64.2Ų
Polar contacts buried
Fraction buried 81.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1669.0Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1037.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)