Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
30.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.71, H-bond role recall 0.57
Reason: no major geometry red flags detected
2 protein-contact clashes
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.979 kcal/mol/HA)
✓ Good fit quality (FQ -9.35)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (30.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-28.398
kcal/mol
LE
-0.979
kcal/mol/HA
Fit Quality
-9.35
FQ (Leeson)
HAC
29
heavy atoms
MW
438
Da
LogP
2.78
cLogP
Interaction summary
HB 9
HY 3
PI 2
CLASH 2
⚠ Exposure 38%
Interaction summary
HB 9
HY 3
PI 2
CLASH 2
⚠ Exposure 38%
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
Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (7/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 18
Buried (contacted) 11
Exposed 7
LogP 2.78
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.514 | Score | -28.398 |
|---|---|---|---|
| Inter norm | -1.010 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 9 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes; moderate strain Δ 30.0 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
GLU274
GLY199
GLY201
GLY236
GLY237
GLY276
HIS197
LYS69
SER200
TYR331
TYR389
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.71 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| HB same residue+role | 4 | HB role recall | 0.57 |
| HB same residue | 4 | HB residue recall | 0.57 |
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 321 | 0.4312888916095546 | -0.855947 | -25.5191 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 307 | 1.303464687200235 | -0.78987 | -18.3238 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 289 | 1.76930837462521 | -1.29932 | -35.9638 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 422 | 2.7545848910139727 | -0.868419 | -24.2502 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 295 | 2.796755929845018 | -1.11058 | -31.8963 | 15 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 377 | 2.9388887475161027 | -0.975895 | -27.6065 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 360 | 3.268268659000955 | -0.926537 | -24.8747 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 346 | 3.7743481783884123 | -0.840004 | -25.3743 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 4.280322512603641 | -0.963547 | -25.3705 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 326 | 4.289068608505349 | -0.759293 | -21.2289 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 340 | 4.374513372828821 | -0.659938 | -21.0777 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 268 | 4.513993838828387 | -1.00962 | -28.398 | 9 | 17 | 15 | 0.79 | 0.57 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.398kcal/mol
Ligand efficiency (LE)
-0.9792kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.348
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
437.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-84.11kcal/mol
Minimised FF energy
-114.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
687.1Ų
Total solvent-accessible surface area of free ligand
BSA total
505.1Ų
Buried surface area upon binding
BSA apolar
364.1Ų
Hydrophobic contacts buried
BSA polar
141.1Ų
Polar contacts buried
Fraction buried
73.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2553.6Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1401.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)